commit: b4487963b83d55df769d8cb6552f692bf970c3d5 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Mon Sep 21 12:40:46 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Sep 21 12:40:46 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4487963
Drop obsolete package Sources unavailable Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/est2uni/ChangeLog | 41 - sci-biology/est2uni/est2uni-0.27.ebuild | 99 --- sci-biology/est2uni/est2uni-9999.ebuild | 114 --- .../est2uni/files/9999-est_clustering.pm.patch | 29 - sci-biology/est2uni/files/9999-pipe_db.pm.patch | 15 - sci-biology/est2uni/files/99est2uni | 3 - sci-biology/est2uni/files/configuration.php.patch | 12 - sci-biology/est2uni/files/est2uni | 3 - sci-biology/est2uni/files/est_annot.pm.patch | 456 ---------- sci-biology/est2uni/files/est_annot_go.pm.patch | 136 --- sci-biology/est2uni/files/est_annot_psnp.pm.patch | 11 - .../files/est_annot_reciprocal_blast.pm.patch | 14 - sci-biology/est2uni/files/est_clustering.pm.patch | 383 -------- sci-biology/est2uni/files/est_prepro.pm.patch | 85 -- .../files/installation_est2uni_perl.txt.patch | 85 -- sci-biology/est2uni/files/mysql_fixes.sql | 3 - sci-biology/est2uni/files/pipe_db.pm.patch | 972 --------------------- sci-biology/est2uni/files/tables.sql.patch | 23 - sci-biology/est2uni/files/tgicl_files.patch | 26 - sci-biology/est2uni/metadata.xml | 9 - 20 files changed, 2519 deletions(-) diff --git a/sci-biology/est2uni/ChangeLog b/sci-biology/est2uni/ChangeLog deleted file mode 100644 index db9015a..0000000 --- a/sci-biology/est2uni/ChangeLog +++ /dev/null @@ -1,41 +0,0 @@ -# ChangeLog for sci-biology/est2uni -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 23 Mar 2015; Marius Brehler <[email protected]> est2uni-0.27.ebuild: - Drop keywords (php:5.3 is hardmasked) - - 24 Sep 2014; Justin Lecher <[email protected]> est2uni-0.27.ebuild: - Bump to EAPI=5 - - 06 Jan 2014; Justin Lecher <[email protected]> est2uni-9999.ebuild, - metadata.xml: - Switch from git-2 to git-r3 - - 22 May 2012; Justin Lecher <[email protected]> est2uni-0.27.ebuild, - est2uni-9999.ebuild: - Bump to EAPI=4, remove unnecessary bits - - 12 Dec 2011; Martin Mokrejs <[email protected]> - est2uni-9999.ebuild: - added configuration.php.patch for VHOSTS setup files/configuration.php.patch - est2uni-9999.ebuild - - 30 Jul 2011; Martin Mokrejs <[email protected]> - +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch, - +est2uni-9999.ebuild: - ebuild cleanup est2uni-0.27.ebuild est2uni-9999.ebuild Manifest - files/9999-est_clustering.pm.patch files/9999-pipe_db.pm.patch - files/99est2uni files/est2uni files/est_annot.pm.patch - files/est_annot_go.pm.patch files/est_annot_psnp.pm.patch - files/est_annot_reciprocal_blast.pm.patch files/est_clustering.pm.patch - files/est_prepro.pm.patch files/installation_est2uni_perl.txt.patch - files/mysql_fixes.sql files/pipe_db.pm.patch files/tables.sql.patch - files/tgicl_files.patch metadata.xml - -*est2uni-9999 (05 Jul 2011) - - 05 Jul 2011; Martin Mokrejs <[email protected]> - +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch, - +est2uni-9999.ebuild: - vim est2uni-9999.ebuild diff --git a/sci-biology/est2uni/est2uni-0.27.ebuild b/sci-biology/est2uni/est2uni-0.27.ebuild deleted file mode 100644 index 112176c..0000000 --- a/sci-biology/est2uni/est2uni-0.27.ebuild +++ /dev/null @@ -1,99 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils perl-module webapp - -DESCRIPTION="Perl-based analysis pipeline including php-based web interface" -HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php"; -SRC_URI=" - http://cichlid.umd.edu/est2uni/est2uni_0.27.tar.gz - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core - http://www.geneontology.org/ontology/gene_ontology.obo - http://www.geneontology.org/doc/GO.terms_and_ids"; - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND} - >=dev-db/mysql-4.1 - dev-lang/php:5.3 - dev-perl/go-perl - sci-biology/bioperl - sci-biology/cap3-bin - sci-biology/estscan - sci-biology/exonerate - <sci-biology/hmmer-3.0 - sci-biology/lucy - sci-biology/ncbi-tools - sci-biology/phred - sci-biology/repeatmasker - sci-biology/seqclean - sci-biology/tgicl - www-servers/apache" - -S="${WORKDIR}"/est2uni - -src_prepare(){ - for f in "${FILESDIR}"/*.pm.patch "${FILESDIR}"/tgicl_files.patch; do - cd perl; epatch $f - done -} - -src_compile(){ - $(tc-getCC) ${CFLAGS} ${LDFLAGS} external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik || die -} - -src_install(){ - mkdir -p "${D}"/opt/est2uni - mv external_software/sputnik/sputnik "${D}"/opt/est2uni || die - - chmod a+rx perl/*.pl perl/*.pm || die - mv perl/* "${D}"/opt/est2uni || die - - doenvd "${FILESDIR}"/99est2uni - - mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs - cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die - - mkdir -p "${D}"/opt/est2uni/test_data || die - mv test_data/* "${D}"/opt/est2uni/test_data || die - # mkdir -p "${D}"/usr/share/"${PN}" || die - # mv test_data "${D}"/usr/share/"${PN}" || die - perl-module_src_install || die - - webapp_src_preinst - webapp_postinst_txt en "${S}"/README - webapp_src_install - - # cp "${DISTDIR}"/UniVec_Core "${DISTDIR}"/UniVec "${D}"/usr/share/ncbi/data/ || die - - einfo "Please follow the pipeline installation and web configuration docs at" - einfo "http://cichlid.umd.edu/est2uni/install.php"; - einfo "BEWARE the software is not maintained anymore by upstream but I do not" - einfo "know any better available (replaced by ngs_backbone which has no web" - einfo "interface yet). Consider using latest svn checkout instead of 0.27" - einfo "release from 2007 or so." - einfo "Possible fixes and stuff to read:" - einfo "https://listas.upv.es/pipermail/est2uni/2008-January/000069.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000103.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000101.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000135.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000131.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-February/000070.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html"; - echo "" - einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary"; -} - -pkg_postinst(){ - webapp_pkg_postinst -} diff --git a/sci-biology/est2uni/est2uni-9999.ebuild b/sci-biology/est2uni/est2uni-9999.ebuild deleted file mode 100644 index 89435ed..0000000 --- a/sci-biology/est2uni/est2uni-9999.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -[ "$PV" == "9999" ] && _GIT=git-r3 - -inherit eutils ${_GIT} perl-module webapp - -DESCRIPTION="Perl-based analysis pipeline including php-based web interface" -HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php"; -if [ "$PV" == "9999" ]; then - EGIT_REPO_URI="git://[email protected]:2203/est2uni.git" - KEYWORDS="" -else - SRC_URI=" - http://cichlid.umd.edu/est2uni/est2uni.tar.gz - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core - http://www.geneontology.org/ontology/gene_ontology.obo - http://www.geneontology.org/doc/GO.terms_and_ids"; - KEYWORDS="~amd64 ~x86" -fi - -SLOT="0" -LICENSE="GPL-3" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND} - >=dev-db/mysql-4.1 - dev-lang/php:5.3 - dev-perl/go-perl - sci-biology/bioperl - sci-biology/cap3-bin - sci-biology/estscan - sci-biology/exonerate - <sci-biology/hmmer-3.0 - sci-biology/lucy - sci-biology/ncbi-tools - sci-biology/phred - sci-biology/repeatmasker - sci-biology/seqclean - sci-biology/tgicl - www-servers/apache" - -S="${WORKDIR}"/est2uni - -src_prepare(){ - for f in "${FILESDIR}"/9999-*.pm.patch; do - cd perl || die - epatch $f - done - cd ../php || die "Failed to chdir to ../php" - epatch "${FILESDIR}"/configuration.php.patch -} - -src_compile(){ - $(tc-getCC) ${CFLAGS} ${LDFLAGS} external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik || die -} - -src_install(){ - dodir /opt/est2uni - mv external_software/sputnik/sputnik "${ED}"/opt/est2uni || die - - chmod a+rx perl/*.pl perl/*.pm || die - mv perl/* "${ED}"/opt/est2uni || die - - doenvd "${FILESDIR}"/99est2uni - - dodir /usr/share/webapps/"${PN}"/"${PV}"/htdocs - cp -r php/* "${ED}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die - - dodir /opt/est2uni/test_data - mv test_data/* "${ED}"/opt/est2uni/test_data || die - # mkdir -p "${D}"/usr/share/"${PN}" || die - # mv test_data "${D}"/usr/share/"${PN}" || die - perl-module_src_install || die - - webapp_src_preinst - webapp_postinst_txt en "${S}"/README - webapp_src_install - # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/temp - # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/blast - - # cp "${DISTDIR}"/UniVec_Core "${DISTDIR}"/UniVec "${D}"/usr/share/ncbi/data/ || die - - einfo "Please follow the pipeline installation and web configuration docs at" - einfo "http://cichlid.umd.edu/est2uni/install.php"; - echo "" - einfo "Example changes to the config file are in ${FILESDIR}/configuration.php.patch" - echo "" - einfo "BEWARE the software is not maintained anymore by upstream but I do not" - einfo "know any better available (replaced by ngs_backbone which has no web" - einfo "interface yet). Consider using latest svn checkout instead of 0.27" - einfo "release from 2007 or so." - einfo "Possible fixes and stuff to read:" - einfo "https://listas.upv.es/pipermail/est2uni/2008-January/000069.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000103.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000101.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000135.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000131.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-February/000070.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html"; - einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html"; - echo "" - einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary"; -} - -pkg_postinst(){ - webapp_pkg_postinst -} diff --git a/sci-biology/est2uni/files/9999-est_clustering.pm.patch b/sci-biology/est2uni/files/9999-est_clustering.pm.patch deleted file mode 100644 index ec38e52..0000000 --- a/sci-biology/est2uni/files/9999-est_clustering.pm.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- perl/est_prepro.pm.ori 2011-02-23 10:56:06.000000000 +0100 -+++ perl/est_prepro.pm 2011-02-23 19:53:13.000000000 +0100 -@@ -499,15 +499,17 @@ - $sth->bind_param(5,$unique_seq_control); - # we get the clone names from the data file - # if not in the data file, we guess it following user specifications in config file -- unless (${%$clone}{$real_name}) { -- ${%$clone}{$real_name}=get_clone_from_est($config,$real_name); -- } -- $sth->bind_param(6,${%$clone}{$real_name}); -- $$seq_info{clone}=${%$clone}{$real_name}; -- if (!${%$clone}{$real_name}){ -- print localtime().": Unable to get clone name for EST $real_name\n"; -- return undef; -- } -+ #unless (${%$clone}{$real_name}) { -+ # ${%$clone}{$real_name}=get_clone_from_est($config,$real_name); -+ #} -+ #$sth->bind_param(6,${%$clone}{$real_name}); -+ #$$seq_info{clone}=${%$clone}{$real_name}; -+ #if (!${%$clone}{$real_name}){ -+ # print localtime().": Unable to get clone name for EST $real_name\n"; -+ # return undef; -+ #} -+ $sth->bind_param(6,'blah'); -+ $$seq_info{clone}='blah'; - } - if (not $qual and not ($unique_seq_control eq 'raw_est' or $unique_seq_control eq 'clean_est')) { - $sth->bind_param(5,$unique_seq_control) diff --git a/sci-biology/est2uni/files/9999-pipe_db.pm.patch b/sci-biology/est2uni/files/9999-pipe_db.pm.patch deleted file mode 100644 index 729c550..0000000 --- a/sci-biology/est2uni/files/9999-pipe_db.pm.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- perl/pipe_db.pm 2011-02-23 18:38:47.000000000 +0100 -+++ pipe_db.pm 2011-02-23 19:41:06.000000000 +0100 -@@ -1468,10 +1468,11 @@ - my $tables=shift; - my $ok=1; - -+ my %t = %$tables; # Can't use string ("38/64") as a HASH ref while "strict refs" in use at /opt/est2uni/pipe_db.pm line 1474. - my $table; - foreach $table(keys %$tables) { - if ($ok) { -- $ok=create_table($db,$table,${%{$tables}}{$table}); -+ $ok=create_table($db,$table,$t{$table}); - if ($ok) { - print localtime().": Table $table created\n"; - } else { diff --git a/sci-biology/est2uni/files/99est2uni b/sci-biology/est2uni/files/99est2uni deleted file mode 100644 index 36176aa..0000000 --- a/sci-biology/est2uni/files/99est2uni +++ /dev/null @@ -1,3 +0,0 @@ -EST2UNI_PERL=/opt/est2uni -PERL5LIB=$PERL5LIB:/opt/est2uni -PATH=$PATH:/opt/est2uni diff --git a/sci-biology/est2uni/files/configuration.php.patch b/sci-biology/est2uni/files/configuration.php.patch deleted file mode 100644 index c973597..0000000 --- a/sci-biology/est2uni/files/configuration.php.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- est2uni/configuration.php.example 2011-02-19 02:05:44.000000000 +0100 -+++ est2uni/configuration.php 2011-12-12 16:07:15.000000000 +0100 -@@ -16,7 +16,7 @@ - $config['web_master_email']="[email protected]"; - - # base directory for web pages at this Apache installation -- $config['apache_dir']="/var/www"; -+ $config['apache_dir']="/var/www/localhost/htdocs/est2uni"; - - # directory name for this group of EST projects - $config['group']= ""; - diff --git a/sci-biology/est2uni/files/est2uni b/sci-biology/est2uni/files/est2uni deleted file mode 100644 index 36176aa..0000000 --- a/sci-biology/est2uni/files/est2uni +++ /dev/null @@ -1,3 +0,0 @@ -EST2UNI_PERL=/opt/est2uni -PERL5LIB=$PERL5LIB:/opt/est2uni -PATH=$PATH:/opt/est2uni diff --git a/sci-biology/est2uni/files/est_annot.pm.patch b/sci-biology/est2uni/files/est_annot.pm.patch deleted file mode 100644 index 3a5b804..0000000 --- a/sci-biology/est2uni/files/est_annot.pm.patch +++ /dev/null @@ -1,456 +0,0 @@ ---- est_annot.pm.ori 2011-02-21 17:19:51.000000000 +0100 -+++ est_annot.pm 2011-02-23 00:06:03.000000000 +0100 -@@ -37,7 +37,7 @@ - sub store_blast_report($$$); #stores a blast report into the mysql database - sub annotate_unigenes_from_db($); #adds to the unigenes table the best hits from the blast reports - sub do_blast_annotation (\@$); #annotates a unigene acording to the blast results obtained for a single database --sub hit_is_not_annoymous ($$); #checks if a hit has one of the annonymous tags -+sub hit_is_not_anonymous ($$); #checks if a hit has one of the annonymous tags - sub store_estscan_orfs($); #Stores the ESTScan results - sub run_hmmer_for_unigenes ($); #runs hmmer for all the unigenes - sub parse_and_store_hmmer($); #parses the hmmer result and stores it in the mysql database -@@ -208,10 +208,10 @@ - - my $dbh=open_db($db) or return 0; - my $st="INSERT INTO $table VALUES (?,?,?,?,?,?);"; -- my $sth=$dbh->prepare($st); -+ my $sth=$dbh->prepare($st) or die localtime().": Error preparing INSERT INTO $table VALUES (?,?,?,?,?,?): $DBI::errstr\n"; - - my $num_micros=0; -- open IN, "<$in_file"; -+ open IN, "<$in_file" or die ocaltime().": Error opening input file $in_file: $!\n"; - my $seq_name; - my $num_micros_seq=0; - while (my $line=<IN>){ -@@ -279,7 +279,7 @@ - my $cmd="$bin -u $max_unit_length -v $min_unit_length -L $min_length_of_ssr $in_file > $out_file"; - not (system ($cmd)) or ( - print localtime().": Something went wrong running Sputnik to find microsatellites\n" and -- print localtime().": Command was: $cmd\n" and -+ print localtime().": Command was: $cmd: $!\n" and - return 0 - ); - return 1; -@@ -322,7 +322,7 @@ - my $sth=prepare_st($dbh,$st) or return 0; - execute_st($sth) or return 0; - open OUT,">$outf" or ( -- print localtime().": There was a problem opening the file $outf as output\n" and -+ print localtime().": There was a problem opening the file $outf as output: $!\n" and - return 0 - ); - while (my @field = $sth->fetchrow_array){ -@@ -371,8 +371,9 @@ - } - my $table=read_config($config,'hmmer_table',''); - my $dbh=open_db($db) or return 0; -- my $st="INSERT INTO $table VALUES ('',?,?,?,?,?,?,?,'');"; -- my $sth=$dbh->prepare($st); -+ my $st="INSERT INTO $table VALUES (NULL,?,?,?,?,?,?,?,NULL);"; -+ print localtime().": Trying to prepare \"$st\" for db=$db and table=$table\n"; -+ my $sth=$dbh->prepare($st) or print localtime().": Error preparing $st statement: $DBI::errstr\n"; - - - my $ok=1; -@@ -427,7 +428,7 @@ - my $out=read_config($config,'hmmer_res',''); - my $micros=read_config($config,'micros',''); - unless ($bin and $db and $out and $micros){ -- print localtime().": Some of the parameters needed by HMMER are missing\n"; -+ print localtime().": Some of the parameters needed by HMMER are missing: $bin, $db, $out, $micros\n"; - return 0; - } - -@@ -439,7 +440,7 @@ - $cmd="$pvmd_bin $host_file &"; - print localtime().": Launching pvm: $cmd\n"; - not (system($cmd)) or ( -- print localtime().": There was a problem launching the pvm environment\n" and -+ print localtime().": There was a problem launching the pvm environment: $!\n" and - return 0 - ); - $cmd="$bin --cpu $micros --pvm $db $in > $out"; -@@ -452,7 +453,7 @@ - stop_pvm($config); - } - if ($not_ok){ -- print localtime().": There was a problem running HMMER\n"; -+ print localtime().": There was a problem running HMMER: $!\n"; - return 0; - } - -@@ -510,8 +511,8 @@ - #begin_orf mediumint unsigned not null, - #end_orf mediumint unsigned not null, - #reverse tinyint(1) not null -- my $st="INSERT INTO $table VALUES ('',?,?,?,?,?,?);"; -- my $sth=$dbh->prepare($st); -+ my $st="INSERT INTO $table VALUES (NULL,?,?,?,?,?,?);"; -+ my $sth=$dbh->prepare($st) or die localtime().": Error preparing $st statement: $DBI::errstr\n"; - - my $no_exit=1; - my $ok=1; -@@ -544,7 +545,7 @@ - } - $sth->execute() or $ok=0; - unless ($ok){ -- print localtime().": There was a problem executing the statement $st\n"; -+ print localtime().": There was a problem executing the statement: $st: $DBI::errstr\n"; - return 0; - } - }else{ -@@ -583,7 +584,7 @@ - my $cmd="$bin $seq_file -M $matrix -t $out_pep -o $out_dna\n"; - not(system($cmd)) or ( - print localtime().": There has been a problem running ESTScan.\n" and -- print localtime().": Command was:\n$cmd\n" and -+ print localtime().": Command was:\n$cmd: $!\n" and - return 0 - ); - -@@ -698,7 +699,7 @@ - if (not ($putative_e_value) or ($e_value < $putative_e_value)){ - #we evaluate if this is a good hit - #is greater than the $inf_limit -- if (($e_value<$inf_limit) and hit_is_not_annoymous($hit,$config)){ -+ if (($e_value<$inf_limit) and hit_is_not_anonymous($hit,$config)){ - #this is a good hit, we should annotate the unigene - $putative_e_value=$e_value; - #we remove the first word and the trailing information of the hit -@@ -718,7 +719,7 @@ - return $putative_annot; - } - --sub hit_is_not_annoymous ($$){ -+sub hit_is_not_anonymous ($$){ - my $hit=shift; - my $config=shift; - my $ok=1; -@@ -730,7 +731,7 @@ - if ($hit =~ /$tag/i) {return 0} - } - -- # hit is also annonymous if it has no description -+ # hit is also anonymous if it has no description - # JF, 2007-01-10 - if ($hit =~ /^\t$/) {return 0} - -@@ -747,7 +748,7 @@ - my $table=read_config($config,'unigenes_table2','') or return 0; - my $st="UPDATE $table SET annotation=NULL;"; - my $dbh=open_db($db) or ( -- print localtime().": Unable to open database $db\n" and -+ print localtime().": Unable to open database $db: $DBI::errstr\n" and - return 0 - ); - my $sth=prepare_st($dbh,$st) or return 0; -@@ -776,7 +777,7 @@ - my $cmd="cp $seq_file $blast_dir".$db_name; - my $fail=system($cmd); - if ($fail){ -- print localtime().": There was a problem with the command: $cmd\n"; -+ print localtime().": There was a problem with the command: $cmd: $!\n"; - return 0; - } - #format the database -@@ -792,7 +793,7 @@ - } - $fail=system($cmd); #now the database is formatted - if ($fail){ -- print localtime().": There was a problem with the command: $cmd\n"; -+ print localtime().": There was a problem with the command: $cmd: $!\n"; - print localtime().": Logfile is $log\n"; - return 0; - } -@@ -986,7 +987,7 @@ - my $in = new Bio::SearchIO(-format => 'blast',-file => $in_file); - open OUT,">$out_file" or $ok=0; - unless ($ok) { -- print localtime().": The out file: $out_file could not be opened.\n"; -+ print localtime().": The out file: $out_file could not be opened: $!\n"; - return 0; - } - -@@ -1092,7 +1093,7 @@ - - #prints a wellcome message - sub wellcome_annot () { -- print localtime().": Wellcome to the EST annotation pipe, have a pleasant jouney.\n\n"; -+ print localtime().": Welcome to the EST annotation pipe, have a pleasant journey.\n\n"; - } - - -@@ -1112,6 +1113,7 @@ - my $dbh=open_db($db) or return 0; - #if the database is superunigenes previous blast superunigenes should be removed - if ($blast_db =~ /superunigenes$/){ -+ print localtime().": Deleting previous BLAST results: DELETE FROM blast_result WHERE db='superunigenes'\n"; - my $st="DELETE FROM blast_result WHERE db='superunigenes'"; - my $sth=$dbh->prepare($st) or return 0; - execute_st($sth) or return 0; -@@ -1129,18 +1131,19 @@ - if ($ext){$temp_in.=$separator.$ext} - - #we create a new in file with the sequences that still has no blast stored in the database -- #if the blast is alredy done, there is no need to repeat it -+ #if the blast is already done, there is no need to repeat it - my $st; - if (read_config($config,'mysql_compress','')){ - $st="SELECT UNCOMPRESS(blast_result) FROM blast_result WHERE query_seq=? AND db='$blast_db'"; - }else{ - $st="SELECT blast_result FROM blast_result WHERE query_seq=? AND db='$blast_db'"; - } -+ print localtime().": Extracting from $in_file those FASTA entries which have no rows matching in blast_result.query_seq using Bio::SeqIO into $temp_in\n"; - my $sth=$dbh->prepare($st) or return 0; - my $num_blast_todo=0; - my $in_seq = Bio::SeqIO->new('-file' => "<$in_file",'-format' => "fasta") or return 0; - my $out_seq = Bio::SeqIO->new('-file' => ">$temp_in",'-format' => "fasta") or return 0; -- open OUT, ">$blast_file_from_db"; -+ open OUT, ">$blast_file_from_db" or print localtime().": Cannot write to $blast_file_from_db file: $!\n"; - while (my $seq=$in_seq->next_seq){ - my $seq_name=$seq->id; - $sth->bind_param(1,$seq_name); -@@ -1162,10 +1165,11 @@ - #we run the blast - #we need to check for every blast if this blast has already been done to avoid repeating blast from different modules - if (!$num_blast_todo){ -- print localtime().": All BLASTs are already on the database\n"; -+ print localtime().": All BLASTs are already in the database: \$num_blast_todo=$num_blast_todo\n"; - my $cmd="mv $blast_file_from_db $out_file"; - !system ($cmd) or return 0; -- return 1 -+ print localtime().": Renamed $blast_file_from_db to $out_file\n"; -+ return 1; - } - run_local_blast($temp_in,$in_type,$blast_file_from_blast,$blast_db,$config) or return 0; - $dbh=open_db($db) or return 0; -@@ -1173,14 +1177,18 @@ - #we split the result and we store it on the database - #we should do a minimal parsing but we don't use bioperl to speed up the process - #we just asume that every blast begins with ^BLAST and that the query is ^Query= xxxxxxxx -- open IN,"<$blast_file_from_blast" or return 0; -+ if (! -r $blast_file_from_blast) { -+ print localtime().": File $blast_file_from_blast is not readable: $!\n"; -+ return 0; -+ } -+ open IN,"<$blast_file_from_blast" or die localtime().": Cannot open $blast_file_from_blast file: $!\n"; - my $more=1; - my $blast_result=""; - my $query=""; - if (read_config($config,'mysql_compress','')){ -- $st="INSERT INTO blast_result (query_seq,db,blast_result) VALUES (?,?,COMPRESS(?))"; -+ $st="INSERT DELAYED INTO blast_result (query_seq,db,blast_result) VALUES (?,?,COMPRESS(?))"; - }else{ -- $st="INSERT INTO blast_result (query_seq,db,blast_result) VALUES (?,?,?)"; -+ $st="INSERT DELAYED INTO blast_result (query_seq,db,blast_result) VALUES (?,?,?)"; - } - $sth=$dbh->prepare($st) or return 0; - while ($more){ -@@ -1211,6 +1219,7 @@ - #now we have two files with blast results, the one generated by the blast and the one made by stored blast - #we should merge them to obtain the output file - my $cmd="cat $blast_file_from_blast $blast_file_from_db > $out_file"; -+ print localtime().": Merging computed blast output with the one already in database: 'cat $blast_file_from_blast $blast_file_from_db > $out_file'\n"; - !system ($cmd) or return 0; - - return 1; -@@ -1241,7 +1250,7 @@ - print localtime().": There was a problem executing the statement:\n" and - print localtime().": Query: $query\n" and - print localtime().": Blast db: $blast_db\n" and -- print localtime().": $st\n" and -+ print localtime().": $st: $DBI::errstr\n" and - return 0 - ); - return 1; -@@ -1267,25 +1276,55 @@ - - my $db;my $db_type; my $env_blastdir; my $program; - if (not($db_name =~ /unigenes\.*\d*/) and $db_name ne 'superunigenes'){ -+ print localtime().": BLAST database $db_name does not match REGEXP with /unigenes\.*\\d*/ nor =='superunigenes',\n\t\t\tfetching its location from table db (sourced from databases.csv)\n"; - $db=${$$db_info{$db_name}}{'local_blast_name'}; - $db_type=${$$db_info{$db_name}}{'kind'}; -+ print localtime().": Inferred $db_type datatype from table db (sourced from databases.csv)\n"; - }else{ -+ # unigenes and superunigenes are DNA datasets generated from this EST dataset -+ # albeit it is ugly these files were written into BLASTDB directory where typically site-wide, public databases exist - if ($ENV{'BLASTDB'}) { #if blastdb enviroment is set -+ print localtime().": BLAST database $db_name will be looked up via BLASTDB=".$ENV{'BLASTDB'}."\n"; - #$env_blastdir = $ENV{'BLASTDB'}; - #$ENV{'BLASTDB'} = ''; - $db=$db_name; #db is just db name - }else{ #otherwise -+ print localtime().": Getting rid of the trailing '_dna' if possible\n"; - $db_name =~ s/_dna$//; # get rid of '_dna' in db name - $db=read_config($config,'blast_dir','').$db_name; #we should add the path to the database -+ print localtime().": BLAST database $db was looked up via est_pipe.conf variable \$blast_dir\n"; - } - $db_type='dna'; -+ print localtime().": Forced 'dna' datatype because unigenes and superunigenes are DNA datasets generated from this EST dataset.\n\t\t\t However, it is ugly that these files were written into BLASTDB defined directory where typically site-wide, public databases exist.\n"; - } - unless (check_blastdb($ENV{'BLASTDB'},$db)) { - print localtime().": BLAST database $db cannot be found at $ENV{'BLASTDB'}\n"; -+ } else { -+ if (-r $ENV{'BLASTDB'}."/".$db) { -+ print localtime().": BLAST database $db exists in $ENV{'BLASTDB'}\n"; -+ if ($db_type eq 'dna') { -+ if (! -r $ENV{'BLASTDB'}."/".$db.".nin") { -+ system("cd $ENV{'BLASTDB'} && formatdb -p F -i $db") or die "Failed to formatdb -p F -i $db\n"; -+ } else { -+ print localtime().": BLAST database ".$ENV{'BLASTDB'}."/".$db." already formatted, good\n"; -+ } -+ } elsif ($db_type eq 'pep') { -+ if (! -r $ENV{'BLASTDB'}."/".$db.".pin") { -+ system("cd $ENV{'BLASTDB'} && formatdb -p T -i $db") or die "Failed to formatdb -p T -i $db\n"; -+ } else { -+ print localtime().": BLAST database ".$ENV{'BLASTDB'}."/".$db." already formatted, good\n"; -+ } -+ } else { -+ print localtime().": Do not know whether $db is a pep/dna database, not checking whether it is formatted by formatdb, it is your job\n"; -+ } -+ } else { -+ print localtime().": Cannot find BLAST database ".$ENV{'BLASTDB'}."/".$db."\n"; -+ return 0; -+ } - } - - if (!$db_type){ -- print localtime().": Database type (dna or pep) not defined for database $db_name\n"; -+ print localtime().": Database type (dna or pep) not defined for database $db_name in databases.csv and subsequently in table db.\n"; - return 0; - } - $program = ${$$db_info{$db_name}}{'blast_program'}; -@@ -1294,6 +1333,7 @@ - elsif ($in_type eq 'pep' and $db_type eq 'dna'){$program='tblastn'} - elsif ($in_type eq 'dna' and $db_type eq 'pep'){$program='blastx'} - elsif ($in_type eq 'pep' and $db_type eq 'pep'){$program='blastp'} -+ else { print localtime().": Wrong combination of input data type=$in_type and db.kind=$in_type, do not know which of blastn/tblastn/blastx/blastp to use\n"; return 0; } - }elsif($program ne'blastn' and $program ne'tblastn' and $program ne'blastx' and $program ne'blastp' and $program ne'tblastx'){ - print localtime().": BLAST program called $program is not allowed\n"; - return 0; -@@ -1330,7 +1370,7 @@ - $ok=not (system("rm $out_file")); - unless ($ok){ - print localtime().": The BLAST output file: $out_file\n"; -- print localtime().": exists and can not be removed\n"; -+ print localtime().": exists and can not be removed: $!\n"; - return 0; - }; - } -@@ -1346,7 +1386,7 @@ - my $fail=system($cmd); - if ($fail){ - print localtime().": Something wen't wrong with the mpiBLAST\n"; -- print localtime().": Command was: $cmd\n"; -+ print localtime().": Command was: $cmd: $!\n"; - return 0; - } - } else { -@@ -1357,7 +1397,7 @@ - my $fail=system($cmd); - if ($fail){ - print localtime().": Something wen't wrong with the BLAST\n"; -- print localtime().": Command was: $cmd\n"; -+ print localtime().": Command was: $cmd: $!\n"; - return 0; - } - }else{ -@@ -1371,7 +1411,7 @@ - #we create the input stream - my $in = Bio::SeqIO->new(-file => $in_file , -format => 'Fasta') or $ok=0; - unless ($ok){ -- print localtime().": There was a problem opening the file $in_file\n"; -+ print localtime().": There was a problem opening the file $in_file: $!\n"; - } - my $seq; my $blast_report; - while ($seq=$in->next_seq()) { -@@ -1380,13 +1420,13 @@ - #input file there could be some memory trouble - $blast_report= $factory->blastall($seq); - unless ($blast_report) { -- print localtime().": There was a problem running the BLAST search\n"; -+ print localtime().": There was a problem running the BLAST search: $!\n"; - return 0; - } -- system("cat $temp_file >> $out_file") -+ system("cat $temp_file >> $out_file") or die "Cannot append to $out_file: $!\n"; - } -- #we remove the temporal file -- system("rm $temp_file"); -+ #we remove the temporary file -+ system("rm $temp_file") or die "Cannot remove temporary file $temp_file: $!\n"; - #my $blast_report = $factory->blastall($in_file); - } - } -@@ -1425,7 +1465,7 @@ - my $blast_dbs=read_config($config,'blast_dbs',''); - my @blast_dbs=split(/,/,$blast_dbs); - unless (@blast_dbs) { -- print localtime().": There are no BLAST databases defined in the config file\n"; -+ print localtime().": There are no BLAST databases defined in the config file under \$blast_dbs\n"; - return 0; - } - #how are the report files named? -@@ -1441,7 +1481,7 @@ - } - my $db=read_config($config,'db_path',''); #complete path to the mysql db - unless (check_table($db,$table)){ -- print localtime().": Table $table for store the BLAST reports is not in database $db\n"; -+ print localtime().": Table $table to store the BLAST reports is not in created in the database $db\n"; - return 0; - } - -@@ -1461,7 +1501,7 @@ - my $config=shift; - my $blast_db=shift; - my $in_file=shift; -- print localtime().": Storing BLAST report: $in_file into the database\n"; -+ print localtime().": Storing BLAST report from $in_file into the database\n"; - my $table=read_config($config,'blast_reports_table',''); - my $db=read_config($config,'db_path',''); #complete path to the mysql db - -@@ -1477,13 +1517,13 @@ - #| identity | float | | | 0 | | - #| similarity | float | | | 0 | | - #| e_value -- my $st="INSERT INTO $table (blast_result_id,subj_acc,description,location_begin_query,location_end_query,location_query,location_begin_subj,location_end_subj,location_subj,identity,similarity,e_value) VALUES (?,?,?,?,?,?,?,?,?,?,?,?);"; -+ my $st="INSERT DELAYED INTO $table (blast_result_id,subj_acc,description,location_begin_query,location_end_query,location_query,location_begin_subj,location_end_subj,location_subj,identity,similarity,e_value) VALUES (?,?,?,?,?,?,?,?,?,?,?,?);"; - my $sth=$dbh->prepare($st) or return 0; - my $st_blast_result="SELECT blast_result_id FROM blast_result WHERE query_seq=? AND db=?"; - my $sth_blast_result=$dbh->prepare($st_blast_result) or return 0; - unless ($sth){ - print localtime().": There was a problem preparing statement:\n"; -- print localtime().": $st\n"; -+ print localtime().": $st: $DBI::errstr\n"; - close_db($dbh); - return 0; - } -@@ -1493,8 +1533,10 @@ - } - open IN, "<$in_file" or $ok=0; - unless ($ok) { -- print localtime()." There was a problem opening file $in_file\n"; -+ print localtime()." There was a problem opening file $in_file: $!\n"; - return 0; -+ } else { -+ print localtime().": Parsing $in_file with BLAST plaintext output\n"; - } - my $line;my $query;my $hit; - while ($ok){ -@@ -1513,7 +1555,7 @@ - if ($array[0]){ - $blast_result_id=$array[0] - }else{ -- print localtime().": BLAST result ID has not been found in the database\n"; -+ print localtime().": BLAST result blast_result_id has not been found in the database using query_seq=$query AND db=$blast_db\n"; - return 0; - } - -@@ -1558,6 +1600,7 @@ - print localtime().": query: $query\n"; - print localtime().": blast_db: $blast_db\n"; - print localtime().": hit: $hit\n"; -+ print localtime().": The error was: $DBI::errstr\n"; - return 0; - } - } diff --git a/sci-biology/est2uni/files/est_annot_go.pm.patch b/sci-biology/est2uni/files/est_annot_go.pm.patch deleted file mode 100644 index bdda596..0000000 --- a/sci-biology/est2uni/files/est_annot_go.pm.patch +++ /dev/null @@ -1,136 +0,0 @@ ---- est_annot_go.pm.ori 2011-02-22 15:33:33.000000000 +0100 -+++ est_annot_go.pm 2011-02-23 00:12:48.000000000 +0100 -@@ -213,13 +213,13 @@ - sub annotate_go_from_blast($$){ - my $config=shift; - my $db_info=shift; -- print localtime().": Annotating the sequences with GO terms looking at the BLAST results.\n"; -+ print localtime().": Annotating the sequences with GO terms from ".read_config($config,'go_assoc_table','')." looking at the BLAST results in ".read_config($config,'go_db_path','').".\n"; - - #the go-blast_db association is stored in a table on a database - my $go_db_path=read_config($config,'go_db_path',''); - my $assoc_table=read_config($config,'go_assoc_table',''); - my $go_dbh=open_db($go_db_path) or ( -- print localtime().": There was a problem opening the database $go_db_path\n" and -+ print localtime().": There was a problem opening the database $go_db_path: $DBI::errstr\n" and - return 0 - ); - -@@ -227,13 +227,13 @@ - my $result_table=read_config($config,'go_table',''); - my $est_db_path=read_config($config,'db_path',''); - my $est_dbh=open_db($est_db_path) or ( -- print localtime().": There was a problem opening the database $est_db_path\n" and -+ print localtime().": There was a problem opening the database $est_db_path: $DBI::errstr\n" and - return 0 - ); - #we use ignore because we're interested just in the first annotation for the combined seq_go_slim, it could be more but they're not important - my $est_st="INSERT IGNORE INTO $result_table (db,db_symbol,qualifier,go_id,ori_evidence,evidence,aspect,taxon_id,e_value,is_slim,seq_id) VALUES (?,?,?,?,?,?,?,?,?,?,?);"; - my $est_sth=prepare_st($est_dbh,$est_st) or ( -- print localtime().": There was a problem executing the statement $est_st\n" and -+ print localtime().": There was a problem executing the statement $est_st: $DBI::errstr\n" and - return 0 - ); - -@@ -255,7 +255,7 @@ - my $real_table=$assoc_table.$go_db; - my $go_st="SELECT db,db_symbol,qualifier,go_id,evidence,aspect,taxon_id,is_slim FROM $real_table WHERE db_symbol=? ;"; - my $go_sth=prepare_st($go_dbh,$go_st) or ( -- print localtime().": There was a problem executing the statement $go_st\n" and -+ print localtime().": There was a problem executing the statement $go_st: $DBI::errstr\n" and - return 0 - ); - unless ($go_db){ -@@ -264,7 +264,7 @@ - } - #we go through the blast files using the bioperl blast parser - my $in = new Bio::SearchIO(-format => 'blast',-file => $blast_file) or( -- print localtime().": There was a problem creating a bioperl handler for the BLAST file $blast_file\n" and -+ print localtime().": There was a problem creating a bioperl handler for the BLAST file $blast_file: $!\n" and - return 0 - ); - -@@ -277,9 +277,12 @@ - my $significative_hit=0; - my $query=$result->query_name; - my $hit=$result->next_hit; -- unless ($hit){$done=1;last}; #if there isn't more hits we're finnished -+ unless ($hit){$done=1;last}; #if there isn't more hits we're finished - my $acc=$hit->name; -- #the arabidopsis project puts an .number in the hit name that should be removed -+ if (! $acc ) { -+ print localtime().": No \$acc value parsed from \$hit->name\n"; -+ } -+ #the arabidopsis project puts a .number in the hit name that should be removed - if (${$$db_info{$go_db}}{'orthologues_arabi_hack'}){ - $acc =~ s/\.\d$//; - } -@@ -299,7 +302,7 @@ - #is there go terms associated with this acc? - $go_sth->bind_param(1,$acc); - $go_sth->execute or ( -- print localtime().": There was a problem executing the statement $go_st with accession $acc\n" and -+ print localtime().": There was a problem executing the statement $go_st with accession $acc: $DBI::errstr\n" and - return 0 - ); - my $there_is_go=0; -@@ -319,7 +322,7 @@ - $est_sth->bind_param(10,$$go[7]); #is this a slim term? - $est_sth->bind_param(11,$query); #annotated sequence - $est_sth->execute or ( -- print localtime().": There was a problem executing the statement $est_st\n" and -+ print localtime().": There was a problem executing the statement $est_st: $DBI::errstr\n" and - return 0 - ); - $done=1; #we do not need any more hits -@@ -333,11 +336,12 @@ - $i_uni++; - } - close_st ($go_sth); -+ print localtime().": $i_uni BLAST unigenes processed from $blast_file, $i_uni_with_go with GO annotations, and $i_go_assoc GO terms associated\n"; - } - close_st ($est_sth); - close_db ($go_dbh); - close_db ($est_dbh); -- print localtime().": $i_uni BLAST unigenes processed, $i_uni_with_go with GO annotations, and $i_go_assoc GO terms associated\n"; -+ print localtime().": $i_uni BLAST unigenes processed from $blast_file_base and "."@go_dbs\n".", $i_uni_with_go with GO annotations, and $i_go_assoc GO terms associated\n"; - return 1; - } - -@@ -367,7 +371,7 @@ - my $assoc_file=${$$db_info{$db}}{'local_go_assoc_file'}; - my $cmd="$bin $slim_file $go_def_file $assoc_file -o $temp_dir$base_out_file".$sep."$db"; - not (system $cmd) or ( -- print localtime().": There was a problem executing: $cmd\n" and -+ print localtime().": There was a problem executing $cmd: $!\n" and - return 0 - ); - $i++; -@@ -447,7 +451,8 @@ - my $table=read_config($config,'go_assoc_table',''); - #now it's time to fill the table with the data - my $real_table=$table.$go_db; -- my $st="INSERT INTO $real_table (db,db_symbol,qualifier,go_id,evidence,aspect,taxon_id,is_slim) VALUES (?,?,?,?,?,?,?,?);"; -+ # this is a wastefull insert inserting qualifier, taxon_id, is_slim equal to NULL -+ my $st="INSERT DELAYED INTO $real_table (db,db_symbol,qualifier,go_id,evidence,aspect,taxon_id,is_slim) VALUES (?,?,?,?,?,?,?,?);"; - my $dbh=open_db($db_path) or ( - print localtime().": There was a problem opening the database $db_path\n" and - return 0 -@@ -491,7 +496,7 @@ - $sth->bind_param(5,$items[6]); #evidence - $sth->bind_param(6,$items[8]); #aspect - $sth->bind_param(7,$items[12]); #taxon_id -- $sth->bind_param(8,$is_slim); -+ $sth->bind_param(8,$is_slim); #is_slim - }else{ - print localtime().": Gene-GO association file has no defined format in $config go_assoc_file_format\n"; - print localtime().": Or the format is not supported. Supported formats are goa and tair\n"; -@@ -542,7 +547,7 @@ - my $db=read_config($config,'db_path',''); - - open IN,"<$file" or ( -- print localtime().": Imposible to open file: $file\n" and -+ print localtime().": Error opening file $file: $!\n" and - return 0 - ); - diff --git a/sci-biology/est2uni/files/est_annot_psnp.pm.patch b/sci-biology/est2uni/files/est_annot_psnp.pm.patch deleted file mode 100644 index 996d625..0000000 --- a/sci-biology/est2uni/files/est_annot_psnp.pm.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- est_annot_psnp.pm.ori 2011-02-22 20:12:25.000000000 +0100 -+++ est_annot_psnp.pm 2011-02-22 20:12:46.000000000 +0100 -@@ -773,7 +773,7 @@ - } - - my $dbh=open_db($db) or return 0; -- my $st_psnp="INSERT INTO $table_psnp (psnp_id,unigene,location,is_snp,is_indel,score,enzymes) VALUES (?,?,?,?,?,?,'');"; -+ my $st_psnp="INSERT INTO $table_psnp (psnp_id,unigene,location,is_snp,is_indel,score,enzymes) VALUES (?,?,?,?,?,?,NULL);"; - my $sth_psnp=$dbh->prepare($st_psnp); - my $st_seq="INSERT INTO $table_seq (psnp_id,nucleotide,est,accession) VALUES (?,?,?,?);"; - my $sth_seq=$dbh->prepare($st_seq); diff --git a/sci-biology/est2uni/files/est_annot_reciprocal_blast.pm.patch b/sci-biology/est2uni/files/est_annot_reciprocal_blast.pm.patch deleted file mode 100644 index e887f7e..0000000 --- a/sci-biology/est2uni/files/est_annot_reciprocal_blast.pm.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- est_annot_reciprocal_blast.pm.ori 2011-02-22 01:19:43.000000000 +0100 -+++ est_annot_reciprocal_blast.pm 2011-02-22 01:39:37.000000000 +0100 -@@ -106,8 +106,9 @@ - my @dbs=split (',',read_config($config,'reci_dbs','')); - foreach my $db (@dbs){ - if (!$$db_info{$db}){ -- print localtime().": Database $db is not defined in db table on the databases\n"; -- return 0; -+ print localtime().": Database $db included in \$reci_dbs is not described in table db, skipping.\n"; -+ #return 0; -+ next; - } - my $in_file=$unigenes_seq_file; - my $outf=$in_file.$separator.$db.$separator."blast"; diff --git a/sci-biology/est2uni/files/est_clustering.pm.patch b/sci-biology/est2uni/files/est_clustering.pm.patch deleted file mode 100644 index a6e553a..0000000 --- a/sci-biology/est2uni/files/est_clustering.pm.patch +++ /dev/null @@ -1,383 +0,0 @@ ---- est_clustering.pm.ori 2011-02-21 13:12:39.000000000 +0100 -+++ est_clustering.pm 2011-02-22 20:23:16.000000000 +0100 -@@ -76,7 +76,7 @@ - } - - sub contig_image ($) { -- print localtime().": Creating contig images\n"; -+ print localtime().": Creating contig images using contigimage.pl\n"; - my $config = shift; - my $bin = read_config($config,'contigimage_bin','contigimage.pl'); - my $ace = read_config($config,'ace_file',''); -@@ -94,6 +94,8 @@ - my $qual_file=read_config($config,'seqclean_masked_qual',''); #output file for the qualities - my $db=read_config($config,'db_path',''); #path to the database in the format dbi:$dbi_driver:$db_name:$host - my @libraries=split(/,/,read_config($config,'libraries','')); #libraries to be retrieved -+ # if populate_clone_table=0 then the clone table is empty, therefore the SELECT would return empty results -+ my $populate_clone_table=read_config($config,'populate_clone_table',''); - my $ok=1; - print localtime().": Fetching processed ESTs from the database\n"; - -@@ -108,20 +110,36 @@ - #we create the handler for the database - my $dbh; my $sth; #database and statements handlers - if ($ok){$dbh=open_db($db) or $ok=0}; #we open the database -- my $st="SELECT sequence.name,sequence.sequence,sequence.quality FROM sequence,est,clone WHERE ( "; -+ -+ my $st=""; -+ if ($populate_clone_table) { -+ $st="SELECT sequence.name,sequence.sequence,sequence.quality FROM sequence,est,clone WHERE ( "; - foreach (@libraries) { - $st.="clone.library = '$_' OR " - } - $_=$st; s/ OR $//;$st=$_; #this removes the trailing OR - $st.=" ) "; -+ } else { -+ $st="SELECT sequence.name,sequence.sequence,sequence.quality FROM sequence,est WHERE "; -+ } -+ -+ # if populate_clone_table=0 then the clone table is empty, therefore the SELECT would return empty results -+ # mysql> SELECT sequence.name,sequence.sequence,sequence.quality FROM sequence,est,clone WHERE -+ # ( clone.library = 'sgn' OR clone.library = 'fake' OR clone.library = 'tigr' ) -+ # AND clone.name=est.clone AND est.processed_seq=sequence.name; -+ # Empty set (0.00 sec) -+ if ($populate_clone_table) { - $st.= "AND clone.name=est.clone AND est.processed_seq=sequence.name"; -+ } else { -+ $st.= "est.processed_seq=sequence.name"; -+ } - - if ($ok) {$sth=$dbh->prepare($st) or $ok=0} - #we execute the statement - if ($ok) { - $sth->execute() or $ok=0; - unless ($ok) { -- print localtime().": There was an error executing the SELECT statement\n"; -+ print localtime().": There was an error executing the SELECT statement: $DBI::errstr\n"; - } - } - #now all the results are written in the output files -@@ -138,6 +156,7 @@ - $seq_stream->write_seq($seq); - $qual_stream->write_seq($seq->qual_obj()); - } -+ print localtime().": Fetched ".$sth->rows()." from the database.\n"; - close_st($sth); - close_db($dbh); - return $ok; -@@ -159,11 +178,11 @@ - ); - my $st="DELETE FROM $table WHERE object_type='contig' OR object_type='singleton';"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": Unable to prepare the statement $st\n" and -+ print localtime().": Unable to prepare the statement $st: $DBI::errstr\n" and - return 0 - ); - $sth->execute or ( -- print localtime().": Unable to execute the statement $st\n" and -+ print localtime().": Unable to execute the statement $st: $DBI::errstr\n" and - return 0 - ); - close_st($sth); -@@ -172,11 +191,11 @@ - - $st="UPDATE $table SET unigene=NULL, location_begin=NULL, location_end=NULL, orientation_fwd=NULL, r_begin_in=NULL, r_end_in=NULL, inserts=NULL;"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": Unable to prepare the statement $st\n" and -+ print localtime().": Unable to prepare the statement $st: $DBI::errstr\n" and - return 0 - ); - $sth->execute or ( -- print localtime().": Unable to execute the statement $st\n" and -+ print localtime().": Unable to execute the statement $st: $DBI::errstr\n" and - return 0 - ); - close_st($sth); -@@ -227,7 +246,7 @@ - - # First we run tgicl - chdir($temp_dir); -- $command="$bin_tgicl ".$in_seq." -q ".$in_qual; -+ $command="$bin_tgicl -F ".$in_seq." -q ".$in_qual; - if ($tgicl_opt) { - $command .= " $tgicl_opt"; - } -@@ -247,19 +266,25 @@ - unless ($tgicl_success) - { - print localtime().": There was a problem running tgicl. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $tgicl_success; - } - - # Now we save the results on the results dir - # file with the reads that form every contig - print localtime().": Saving the tgicl contigs results\n"; -+ if (-r $in_seq.$contigs_ext) { -+ # files from older tgicl are *_clusters - $command="mv ".$in_seq.$contigs_ext." ".$contigs_file; -+ } elsif (-r $in_seq."_cl".$contigs_ext) { -+ # files from newer tgicl are *_cl_clusters -+ $command="mv ".$in_seq."_cl".$contigs_ext." ".$contigs_file; -+ } - $tgicl_success= not(system($command)); - unless ($tgicl_success) - { - print localtime().": There was a problem moving the tgicl result. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $tgicl_success; - } - -@@ -270,7 +295,7 @@ - unless ($tgicl_success) - { - print localtime().": There was a problem running tgicl. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $tgicl_success; - } - -@@ -286,7 +311,7 @@ - unless ($tgicl_success) - { - print localtime().": There was a problem running tgicl. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $tgicl_success; - } - -@@ -302,7 +327,7 @@ - unless ($tgicl_success) - { - print localtime().": There was a problem running tgicl. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $tgicl_success; - } - -@@ -313,7 +338,7 @@ - $tgicl_success=not(system($command)); - unless ($tgicl_success) - { -- print localtime().": There was a problem running cdbyank\n"; -+ print localtime().": There was a problem running $command: $!\n"; - return $tgicl_success; - } - -@@ -353,7 +378,7 @@ - $ok=not(system($command)); - unless ($ok) { - print localtime().": There was a problem running cap3. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $ok; - } - my $qual_file=$seq_file.".qual"; -@@ -361,7 +386,7 @@ - system($command); - unless ($ok) { - print localtime().": There was a problem running cap3. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $ok; - } - -@@ -390,7 +415,7 @@ - unless ($ok) - { - print localtime().": There was a problem running cap3. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $ok; - } - -@@ -402,7 +427,7 @@ - unless ($ok) - { - print localtime().": There was a problem running cap3. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $ok; - } - -@@ -412,7 +437,7 @@ - unless ($ok) - { - print localtime().": There was a problem running tgicl. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $ok; - } - -@@ -423,7 +448,7 @@ - unless ($ok) - { - print localtime().": There was a problem running tgicl. The command was:\n"; -- print "$command\n"; -+ print "$command: $!\n"; - return $ok; - } - -@@ -442,17 +467,19 @@ - #we should keep the original singletons names - my $single_file=read_config($config,'singletons_list',''); - my $ori_single_file=read_config($config,'original_singletons_list',''); -+ -+ my $prefix=read_config($config,'prefix',''); -+ my $postfix=read_config($config,'postfix',''); -+ # doh, but the routine update_est_table_with_singletons() anyways looks for the unchanged original file - my $cmd="cp $single_file $ori_single_file"; - my $not_ok=system ($cmd); - if ($not_ok){ -- print localtime()."; There was a problem with the command $cmd\n"; -+ print localtime()."; There was a problem with the command $cmd: $!\n"; - return 0; - } -- my $prefix=read_config($config,'prefix',''); -- my $postfix=read_config($config,'postfix',''); - unless ($prefix or $postfix){ -- print localtime().": WARNING, there are no prefix or postfix to change unigene name\n"; -- print localtime().": WARNING, it won't be any name change\n"; -+ print localtime().": WARNING, there are no prefix or postfix defined to change unigene name\n"; -+ print localtime().": WARNING, there won't be any name change\n"; - return 1; - } - change_seq_names_in_file($contigs_file,$config,'') or return 0; -@@ -470,8 +497,8 @@ - my $postfix=read_config($config,'singleton_seq_tag',''); - - my $temp_file=select_temp_file($config); -- open IN, "<$file"; -- open OUT, ">$temp_file\n"; -+ open IN, "<$file" or die "Error: failed to open $file: $!\n"; -+ open OUT, ">$temp_file" or die "Error: failed to write $temp_file: $!\n"; - while (my $line = <IN>){ - #for fasta files - if ($line =~ /^>/){ -@@ -586,7 +613,7 @@ - my $ok=1; - open OUT,">$outf" or $ok= 0; - unless ($ok){ -- print localtime().": There was a problem opening the file: $outf\n"; -+ print localtime().": There was a problem opening the file: $outf: $!\n"; - return 0; - } - -@@ -629,7 +656,7 @@ - my $ok=1; - open IN, "<$dnaf" or $ok=0; - unless ($ok){ -- print localtime().": ESTScan result file $dnaf couldn't be opened\n"; -+ print localtime().": ESTScan result file $dnaf couldn't be opened: $!\n"; - return 0; - } - while (<IN>){ -@@ -653,18 +680,18 @@ - my $backf=$revf.".bak"; - my $not_ok=system ("cp $revf $backf"); - if ($not_ok){ -- print localtime().": There was a problem when trying to do a copy of $revf to $backf\n"; -+ print localtime().": There was a problem when trying to do a copy of $revf to $backf: $!\n"; - return 0; - } - - open OUT, ">$revf" or $ok=0; - unless ($ok){ -- print localtime().": Reverse file $revf couldn't be opened for output\n"; -+ print localtime().": Reverse file $revf couldn't be opened for output: $!\n"; - return 0; - } - open IN, "<$backf" or $ok=0; - unless ($ok){ -- print localtime().": Reverse file $backf couldn't be opened for input\n"; -+ print localtime().": Reverse file $backf couldn't be opened for input: $!\n"; - return 0; - } - while (<IN>){ -@@ -711,20 +738,20 @@ - - open ACE, "<$ace_file" or $ok=0; - unless ($ok) { -- print localtime().": There has been a problem opening the file $ace_file\n"; -+ print localtime().": There has been a problem opening the file $ace_file: $!\n"; - print localtime().": Maybe is not in the correct tgicl_ace format.\n"; - return 0; - } - - my $dbh=open_db($db); - unless ($dbh) { -- print localtime().": Database $dbh is not reachable\n"; -+ print localtime().": Database $dbh is not reachable: $DBI::errstr\n"; - return 0; - } - my $st= write_insert_st ($table,@fields); - my $sth=prepare_st($dbh,$st); - unless ($sth) { -- print localtime().": There has been a problem preparing the statement: $st\n"; -+ print localtime().": There has been a problem preparing the statement: $st: $DBI::errstr\n"; - close_db($dbh); - return 0; - } -@@ -839,6 +866,10 @@ - push(@$orientation,$1); - } - $contig =~ s/^\n+//; -+ while ($contig =~ s/^BS\s+?\d+\s+?\d+\s+?([^\s]+)\s*\n//){ -+ print localtime().": Skipping BS line in the ACE output due to newer cap3: https://listas.upv.es/pipermail/est2uni/2008-October/000191.html\n";; -+ } -+ $contig =~ s/^\n+//; - my $read_len=[]; my $seq_names=[]; - my $r_begin_in_read=[]; - my $r_end_in_read=[]; -@@ -955,7 +986,7 @@ - $table=read_config($config,'est_table',''); - $st="UPDATE $table SET unigene=?,orientation_fwd=?,location_begin=?,location_end=?,r_begin_in=?,r_end_in=?,inserts=? WHERE processed_seq=?"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st\n" and -+ print localtime().": There was a problem preparing the statement: $st: $DBI::errstr\n" and - return 0 - ); - foreach my $contig_info (@contig_est_info){ -@@ -981,7 +1012,7 @@ - $sth->bind_param(7,$insertion); - $sth->bind_param(8,$seq_name); - $sth->execute or ( -- print localtime().": There was a problem executing the statement $st\n" and -+ print localtime().": There was a problem executing the statement: $st: $DBI::errstr\n" and - return 0 - ); - unless (@{${$contig_info}[1]} and @{${$contig_info}[2]} and @{${$contig_info}[3]}){ -@@ -1042,19 +1073,19 @@ - my $db=read_config($config,'db_path',''); - my $dbh=open_db($db); - unless ($dbh) { -- print localtime().": Database $dbh is not reachable\n"; -+ print localtime().": Database $dbh is not reachable: $DBI::errstr\n"; - return 0; - } - my $st="UPDATE $est_table SET unigene=?,orientation_fwd=1,location_begin=1,location_end=?,r_begin_in=1,r_end_in=? WHERE processed_seq=?"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st\n" and -+ print localtime().": There was a problem preparing the statement: $st: $DBI::errstr\n" and - return 0 - ); - - my $singletons_file=read_config($config,'seq_singletons_file',''); #singletons fasta file - my $ori_singletons_file=read_config($config,'original_singletons_list',''); #singletons list file without the name change this is in fact the name of the est sequences that correspond to every singleton - open ORI, "<$ori_singletons_file" or ( -- print localtime().": There was a problem opening file: $ori_singletons_file\n" and -+ print localtime().": There was a problem opening file: $ori_singletons_file: $!\n" and - return 0 - ); - -@@ -1070,7 +1101,7 @@ - $sth->bind_param(3,$len); - $sth->bind_param(4,$ori_line); - $sth->execute or ( -- print localtime().": There was a problem executing the statement $st\n" and -+ print localtime().": There was a problem executing the statement: $st: $DBI::errstr\n" and - return 0 - ); - } diff --git a/sci-biology/est2uni/files/est_prepro.pm.patch b/sci-biology/est2uni/files/est_prepro.pm.patch deleted file mode 100644 index 7efcbe8..0000000 --- a/sci-biology/est2uni/files/est_prepro.pm.patch +++ /dev/null @@ -1,85 +0,0 @@ ---- est_prepro.pm.ori 2011-02-21 11:37:20.000000000 +0100 -+++ est_prepro.pm 2011-02-22 00:46:57.000000000 +0100 -@@ -478,7 +478,7 @@ - } - else { - print localtime()." There is a problem with the length in sequence ".$temp_seq->id."\n"; -- print localtime()." from file: $seq_file\n. Quality and sequence length don't match.\n"; -+ print localtime()." from file: $seq_file. Quality $temp_qual->length and sequence $temp_seq->length length don't match.\n"; - #print $temp_seq->desc."\n"; - return 0; - } -@@ -973,7 +973,7 @@ - #check that $assignments_file exist - if (not(-r $assi_file)){ - print localtime().": ######################################################################\n"; -- print localtime().": WARNING: Assignment file for lucy is not found or not defined\n"; -+ print localtime().": WARNING: Assignment file $assi_file for lucy is not found or not defined\n"; - print localtime().": Lucy will not be used in the preprocessing\n"; - print localtime().": ######################################################################\n"; - }else{ -@@ -1062,7 +1062,7 @@ - my $tag=read_config($config,'assignment_tag',''); - $command="echo $tag".$library.">> $temp_log"; - chdir ($temp_dir); #we change the directory becouse lucy write some stuff in the working directory -- system($command); -+ system($command) or die print localtime().": $command failed: $!\n"; - chdir ($actual_dir); - # Options used: - # $in_seq fasta sequences generated by phred -@@ -1086,9 +1086,9 @@ - - # lucy log is moved to the results directory - $command="cat $temp_log >> $log"; -- system($command); -+ system($command) or die print localtime().": failed to append $temp_log contents to $log\n"; - $command="rm $temp_log"; -- system($command); -+ system($command) or die print localtime().": failed to delete $temp_log\n"; - - if ($success) - { -@@ -1112,8 +1112,8 @@ - print localtime().": Parsing the lucy output\n"; - # now we check that the input file is in place - unless (check_file($lucy_log_file,"lucy log file")){ -- print localtime().": WARNING there is no lucy log file\n"; -- print localtime().": Maybe lucy has not been used by any library\n"; -+ print localtime().": WARNING there is no lucy log file $lucy_log_file\n"; -+ print localtime().": Maybe lucy has not been used by any library?\n"; - return 1; - } - -@@ -1490,7 +1490,7 @@ - sub run_seqclean($$$$$$$$$$$$) - { - my $config=shift; -- my $library=shift; # informational porpouse only -+ my $library=shift; # informational purpose only - my $trimmed_fasta_file=shift; # name for the trimmed sequences file - my $trimmed_qual_file=shift; # name for the trimmed quality file - my $seqclean_report_file=shift; # report file with the masked area -@@ -1518,7 +1518,13 @@ - #The file with the vector (univec recommended) - my $vec_file=read_config($config,'seqclean_vec_dat',''); - unless (check_file($vec_file,"vector database")){return 0}; -- -+ if (! -r $vec_file.".nin") { -+ print localtime().": Formatting database with formatdb -p F -i $vec_file\n"; -+ system("cd `dirname $vec_file` && formatdb -p F -i $vec_file"); -+ if (! -r $vec_file.".nin") { -+ die "Failed to formatdb $vec_file: $!\n"; -+ } -+ } - my $seqclean_success=1; # control variable - my $command; - my $temp; -@@ -1749,7 +1755,7 @@ - sub seqclean_masking_assignments ($$$$$$) - { - my $config=shift; -- print localtime().": Masking the sequences following seqclean's recomendations\n"; -+ print localtime().": Masking the sequences following seqclean's recommendations\n"; - my @libraries=split(',',read_config($config,'libraries','')); # libraries names - my $report=read_config($config,'seqclean_report',''); # base name for the report generated by seqclean, this is the file with the instruccions for masking the sequences - my $in_seq=shift; # base name for the trimmed sequences file generated by lucy diff --git a/sci-biology/est2uni/files/installation_est2uni_perl.txt.patch b/sci-biology/est2uni/files/installation_est2uni_perl.txt.patch deleted file mode 100644 index a4d2413..0000000 --- a/sci-biology/est2uni/files/installation_est2uni_perl.txt.patch +++ /dev/null @@ -1,85 +0,0 @@ ---- installation_est2uni_perl.txt.ori 2011-02-21 11:52:15.000000000 +0100 -+++ installation_est2uni_perl.txt 2011-02-21 22:58:23.000000000 +0100 -@@ -84,8 +84,12 @@ - .qual. - - There are some library examples on the 'test_data' directory of the EST2uni --distribution. You could just copy that libraries to check the software. Be --aware that the sgn chromatograms could need a modification in the phredpar.dat file -+distribution. You could just copy that libraries to check the software. -+ -+ > cp /usr/local/est2uni/test_data/libraries/* ./libraries -+ > cp -r /usr/local/est2uni/test_data/data . -+ -+Be aware that the sgn chromatograms could need a modification in the phredpar.dat file - (see installation instructions for phred in docs/installation_external_software.txt). - - 4.- Copy the estpipe.conf.example file from the installation directory into -@@ -205,7 +209,7 @@ - Although the clustering software could consider that two unigenes are not similar - enough to be merged, it is useful to know which are these similar clusters of unigenes. - Accordingly, EST2uni does a clustering of the unigenes, and these clusters are named --'superunigenes'. This analysis is done thorough a BLAST search, followed by -+'superunigenes'. This analysis is done through a BLAST search, followed by - parsing the results. Unigenes with a similarity high enough (above user-defined threshold - parameters) are then clustered in a superunigene. - -@@ -219,15 +223,17 @@ - - In EST2uni a database can have several aspects like the blast indexed files, the fasta - sequence files or the related GO files. This information should be placed in the file --referenced by the parameter databases_dat. This file should be uploaded to the database --setting the parameters populate_database_table and do_prior_data_population to 1. -+referenced by the parameter databases_dat, usually named databases.csv. -+Contents of this file will be uploaded into the database when the parameters -+populate_database_table and do_prior_data_population are set to 1. - - In that file, the name of the database is defined in the field "name" and could be different - than the BLAST name. For instance the database name could be "arabidopsis" and the local --BLAST name could be "tair6". When a BLAST against database "arabidopsis" is --asked, EST2uni will look for the local BLAST name in the database. In this example the blast should --be asked for the database "arabidopsis", not against "tair6", despite the fact that the --local blast database is named "tair6". -+BLAST filename could be "tair6". When a BLAST against database "arabidopsis" is -+asked, EST2uni will look for the local BLAST-formatted filenames tair6.* in the BLASTDB -+of $blast_dir directory. In this example the blast should be asked for the database -+"arabidopsis", not against "tair6", despite the fact that the local blast database is -+named "tair6". - - - BLAST ANNOTATION -@@ -243,7 +249,8 @@ - this example the arabidopsis database should be defined in the databases_dat file. On that - file the field local_blast_name should be the name given to that database on the local blast - installation. For instance it could be named tair6. That means that the name in the blast_dbs --parameter and the name of the database in the local blast installation could be different. -+parameter and the name of the database in the local blast installation could be different -+(they are mapped via the databases.csv trick). - - Other important field in the databases file is "kind", which should be set to dna or pep. - -@@ -357,7 +364,7 @@ - same database. The paths for these files should be specified in the local_go_assoc_file and - local_go_slim_obo_file of the databases information file. The GO association file for the - arabidopsis database can be downloaded from the www.arabidopsis.org site. At the time of -- this writting the file is located in: -+ this writing the file is located in: - ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/ATH_GO_GOSLIM.20061021.txt - The GO slim obo file for arabidopsis and goa is on the Gene Ontology ftp: - ftp://ftp.geneontology.org/pub/go/GO_slims/go_slim_plant.obo -@@ -376,7 +383,7 @@ - ---------------- - - You just need to set the parameter do_hmmer_annot to 1 and to set the name --of the HMMER database on the parameter pfam_db. -+of the HMMER database on the parameter pfam_db with a full path. - - HMMER uses the ORFs as a starting point, so it is necessary to have the annotated - ORF already in the database or to ask for the do_estscan_annot. -@@ -400,5 +407,5 @@ - --------------------------- - - Every researcher can be associated with several ESTs using the csv file defined in the working_on_dat --parameter. Those relationships will get loaded when the parameters populate_workin_on_table and -+parameter. Those relationships will get loaded when the parameters populate_working_on_table and - do_prior_data_population are set to 1. diff --git a/sci-biology/est2uni/files/mysql_fixes.sql b/sci-biology/est2uni/files/mysql_fixes.sql deleted file mode 100644 index ee3ec93..0000000 --- a/sci-biology/est2uni/files/mysql_fixes.sql +++ /dev/null @@ -1,3 +0,0 @@ -alter table db change kind kind enum('dna','pep') default null; -alter table db change blast_program blast_program enum('blastn', 'blastp', 'blastx', 'tblastn', 'tblastx') default null; -alter table db change rec_sim_type rec_sim_type enum('orthologue', 'synonymous') default null; diff --git a/sci-biology/est2uni/files/pipe_db.pm.patch b/sci-biology/est2uni/files/pipe_db.pm.patch deleted file mode 100644 index 139cf56..0000000 --- a/sci-biology/est2uni/files/pipe_db.pm.patch +++ /dev/null @@ -1,972 +0,0 @@ ---- pipe_db.pm.ori 2011-02-22 18:08:58.000000000 +0100 -+++ pipe_db.pm 2011-02-22 14:48:03.000000000 +0100 -@@ -90,29 +90,29 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - - #the location statistics - my $st="INSERT INTO pssr_location_view SELECT CASE ((ssr_end<orf_begin)*1+(ssr_begin>orf_end)*2+(ssr_begin>orf_begin && ssr_end<orf_end)*3) WHEN 0 THEN 'other' WHEN 1 THEN '5_utr' WHEN 2 THEN '3_utr' WHEN 3 THEN 'in_orf' END AS location,count(*) AS count FROM ESTScan_orf,sputnik_ssr WHERE sputnik_ssr.seq_name=ESTScan_orf.seq_name GROUP BY (ssr_end<orf_begin)*1+(ssr_begin>orf_end)*2+(ssr_begin>orf_begin && ssr_end<orf_end)*3"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - #the unit kind statistics - $st="INSERT INTO pssr_kind_view SELECT unit,count(*) AS count FROM sputnik_ssr GROUP BY unit"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -128,18 +128,18 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - - #we calculate the min, max and average unigene length - my $st="SELECT MIN(length) AS min_seq_len, MAX(length) AS max_seq_len, AVG(length) AS avg_seq_len FROM sequence WHERE object_type='contig' OR object_type='singleton'"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my $min;my $max;my $avg; -@@ -154,11 +154,11 @@ - } - $st="INSERT unigene_structure_annotation_view (min_seq_len,max_seq_len,avg_seq_len) VALUES ($min,$max,$avg)"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -173,20 +173,20 @@ - #we calculate the min, max and average num ESTs per unigene - $st='CREATE TEMPORARY TABLE est_per_unigene SELECT count(*) AS num_est,unigene FROM est WHERE unigene IS NOT NULL GROUP BY unigene'; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my $st='SELECT MAX(num_est) AS max_num_est, AVG(num_est) AS avg_num_est FROM est_per_unigene'; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - while (my @record=$sth->fetchrow_array){ -@@ -196,11 +196,11 @@ - close_st($sth); - $st="UPDATE unigene_structure_annotation_view SET max_est=$max,avg_est=$avg"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -213,11 +213,11 @@ - #now the annotated unigenes - my $st="SELECT COUNT(*) FROM sequence WHERE annotation IS NOT NULL AND (object_type='contig' OR object_type='singleton')"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my @record=$sth->fetchrow_array; -@@ -225,22 +225,22 @@ - close_st($sth); - $st="UPDATE unigene_structure_annotation_view SET n_uni_with_annot=$n_annot"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - #now the full len - my $st="SELECT COUNT(*) FROM sequence WHERE full_length IS NOT NULL AND (object_type='contig' OR object_type='singleton')"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - @record=$sth->fetchrow_array; -@@ -248,11 +248,11 @@ - close_st($sth); - $st="UPDATE unigene_structure_annotation_view SET n_uni_with_full_len=$n_annot"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -263,14 +263,14 @@ - my $dbh=shift; - my $values=shift; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - my $i=1; - foreach my $value (@$values){ - $sth->bind_param($i,$value); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - $i++; -@@ -282,7 +282,7 @@ - my $dbh=shift; - my $intervals=shift; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - my $bottom; -@@ -293,7 +293,7 @@ - $sth->bind_param(1,$bottom); - $sth->bind_param(2,$top); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my @record=$sth->fetchrow_array; -@@ -329,16 +329,16 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - my $st="INSERT psnp_accessions_view (accession) SELECT DISTINCT accession FROM putative_snp_seq"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -354,26 +354,26 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - my $st="CREATE TEMPORARY TABLE psnp_mutations_temp (nucleotides CHAR(10),is_snp BOOL,INDEX(nucleotides,is_snp)) SELECT GROUP_CONCAT(DISTINCT(putative_snp_seq.nucleotide) ORDER BY putative_snp_seq.nucleotide) AS nucleotides,putative_snp.is_snp FROM putative_snp_seq,putative_snp WHERE putative_snp_seq.psnp_id=putative_snp.psnp_id AND putative_snp_seq.nucleotide!='*' AND putative_snp.is_indel=0 GROUP BY putative_snp_seq.psnp_id"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - $st="INSERT INTO psnp_mutations_view (mutations,is_snp,count) SELECT nucleotides,is_snp,COUNT(*) AS count FROM psnp_mutations_temp WHERE LENGTH(nucleotides)=3 GROUP BY nucleotides,is_snp"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -389,16 +389,16 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - my $st="INSERT reciprocal_species_view (species,type) SELECT species,type FROM reciprocal_similar_sequences GROUP BY species"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -416,46 +416,46 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - my $st="INSERT INTO go_uni_aspect_view (db,aspect,num_unigenes,word) SELECT go.db,go.aspect,count(DISTINCT go.seq_id) AS num_unigenes, CONCAT(go.aspect,go.db) AS word FROM clone,go,est WHERE est.clone=clone.name AND go.seq_id=est.unigene AND go.is_slim=1 GROUP BY word"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - $st="INSERT INTO go_uni_aspect_library_view (db,aspect,library,num_unigenes,word) SELECT go.db,go.aspect,clone.library,count(DISTINCT go.seq_id) AS num_unigenes, CONCAT(go.aspect,go.db,clone.library) AS word FROM clone,go,est WHERE est.clone=clone.name AND go.seq_id=est.unigene AND go.is_slim=1 GROUP BY word"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - $st="INSERT INTO go_term_aspect_view (db,aspect,go_id,definition,num_go,word) SELECT db,go.aspect,go.go_id,definition,count(DISTINCT go.seq_id) AS num_go, CONCAT(go.go_id,go.aspect,db) AS word FROM go,go_def WHERE is_slim=1 AND go_def.go_id=go.go_id GROUP BY word"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - $st="INSERT INTO go_term_aspect_library_view (db,aspect,go_id,definition,library,num_go,word) SELECT db,go.aspect,go.go_id,definition,clone.library,count(DISTINCT go.seq_id) AS num_go, CONCAT(go.go_id,go.aspect,db,clone.library) AS word FROM go,go_def,est,clone WHERE is_slim=1 AND go_def.go_id=go.go_id AND go.seq_id=est.unigene AND est.clone=clone.name GROUP BY word"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -473,27 +473,27 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - my $st="CREATE TEMPORARY TABLE super_count (INDEX(type)) SELECT superunigene,count(*)>1 AS type FROM superunigene GROUP BY superunigene"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - - $st="INSERT INTO superunigene_view (type,num_superunigenes) SELECT type,count(*) AS num_superunigenes FROM super_count GROUP BY type"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -510,17 +510,17 @@ - - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - - my $st="INSERT INTO unigene_view (type,num_unigenes) SELECT object_type,count(*) AS num_unigenes FROM sequence WHERE object_type='contig' OR object_type='singleton' GROUP BY object_type"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); -@@ -539,7 +539,7 @@ - clean_tables($config,@table) or return 0; - my $db=read_config($config,'db_path',''); #database in the form dbi:$dbi_driver:$db_name:$host - my $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - -@@ -547,11 +547,11 @@ - #clones per library - my $st="SELECT clone.library,COUNT(distinct clone.name) AS num_clones FROM clone GROUP BY clone.library"; - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %clones; -@@ -563,11 +563,11 @@ - #raw_est per library - $st="SELECT clone.library,COUNT(*) AS num_raw_est FROM est,clone WHERE est.clone=clone.name AND raw_seq IS NOT NULL GROUP BY clone.library"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %raw_est; -@@ -579,11 +579,11 @@ - #clean_est per library - $st='SELECT clone.library,COUNT(*) AS num_clean_est,AVG(sequence.length) AS mean_length,STD(sequence.length) AS std_dev FROM est,sequence,clone WHERE est.processed_seq=sequence.name AND est.clone=clone.name GROUP BY clone.library;'; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %clean_est; -@@ -599,11 +599,11 @@ - #singletons per library - $st="SELECT clone.library,COUNT(distinct sequence.name) AS num_singletons FROM clone,sequence,est WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='singleton' GROUP BY clone.library"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %singletons; -@@ -615,11 +615,11 @@ - #contigs per library - $st="SELECT clone.library,COUNT(distinct sequence.name) AS num_contigs FROM clone,sequence,est WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='contig' GROUP BY clone.library"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %contigs; -@@ -631,11 +631,11 @@ - #unigenes per library - $st="SELECT clone.library,COUNT(distinct unigene) AS num_unigenes FROM est,clone WHERE est.clone=clone.name GROUP BY clone.library"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %unigenes; -@@ -647,11 +647,11 @@ - #full length per library - $st="SELECT clone.library,COUNT(distinct sequence.name) AS num_full_len FROM clone,sequence,est WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.full_length IS NOT NULL GROUP BY clone.library"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %full_len; -@@ -663,21 +663,21 @@ - #spec unigenes length per library - $st="CREATE TEMPORARY TABLE uni_library_count (PRIMARY KEY(name), INDEX (num_lib))SELECT sequence.name, COUNT(DISTINCT clone.library) AS num_lib, clone.library AS lib_concat FROM sequence,est,clone WHERE sequence.name=est.unigene AND est.clone=clone.name GROUP BY sequence.name"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - $st="SELECT lib_concat as library,COUNT(*) AS num_unigenes_ex FROM uni_library_count WHERE num_lib=1 GROUP BY lib_concat"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %spec_unigenes; -@@ -689,21 +689,21 @@ - #spec contigs per library - $st="CREATE TEMPORARY TABLE contig_library_count (PRIMARY KEY(name), INDEX (num_lib))SELECT sequence.name, COUNT(DISTINCT clone.library) AS num_lib, clone.library AS lib_concat FROM sequence,est,clone WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='contig' GROUP BY sequence.name"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - $st="SELECT lib_concat as library,COUNT(*) AS num_contigs_ex FROM contig_library_count WHERE num_lib=1 GROUP BY lib_concat"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %spec_contigs; -@@ -715,21 +715,21 @@ - #spec singletons per library - $st="CREATE TEMPORARY TABLE singleton_library_count (PRIMARY KEY(name), INDEX (num_lib))SELECT sequence.name, COUNT(DISTINCT clone.library) AS num_lib, clone.library AS lib_concat FROM sequence,est,clone WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='singleton' GROUP BY sequence.name"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - close_st($sth); - $st="SELECT lib_concat as library,COUNT(*) AS num_singletons_ex FROM singleton_library_count WHERE num_lib=1 GROUP BY lib_concat"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - my %spec_singletons; -@@ -742,7 +742,7 @@ - #now we have all the data and we should store it in the view - $st="INSERT INTO library_view (library, num_clones, num_raw_est, num_clean_est, num_singletons, num_contigs, num_unigenes, num_full_len, num_spec_singletons, num_spec_contigs, num_spec_unigenes,avg_est_len,std_est_len) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?)"; - $sth=prepare_st($dbh,$st) or ( -- print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem preparing the statement $st" and - return 0 - ); - foreach my $lib (keys(%libraries)){ -@@ -760,7 +760,7 @@ - $sth->bind_param(12,$avg_est_len{$lib}); - $sth->bind_param(13,$std_est_len{$lib}); - execute_st($sth) or ( -- print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and -+ print localtime().": There was a problem executing the statement $st" and - return 0 - ); - } -@@ -776,12 +776,12 @@ - my $config=shift; - my $dir = $$config{'chromat_dir'}; - opendir DIR,$dir or ( -- print localtime().": It was not possible to open the chromat directory $dir: $!\n" and -+ print localtime().": It was not possible to open the chromat directory: $dir\n" and - return 0 - ); - my @libraries = grep {/^[^\.]/} readdir(DIR); - if (!$libraries[0]){ -- print localtime().": No libraries found in the libraries directory $dir: $!\n"; -+ print localtime().": No libraries found in the libraries directory: $dir\n"; - return 0; - } - close DIR; -@@ -791,18 +791,18 @@ - my $db=read_config($config,'db_path',''); - my $dbh=open_db($db); - unless ($dbh) { -- print localtime().": Database $dbh is not reachable: $DBI::errstr\n"; -+ print localtime().": Database $dbh is not reachable\n"; - return 0; - } - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": Unable to prepare statement: $st: $DBI::errstr\n" and -+ print localtime().": Unable to prepare statement: $st\n" and - return 0 - ); - foreach my $lib (@libraries){ - $sth->bind_param(1,$lib); - $sth->execute() or ( - print localtime().": There was a problem executing the statement:\n" and -- print localtime().": $st: : $DBI::errstr\n" and -+ print localtime().": $st:\n" and - print localtime().": with the library $lib:\n" and - return 0 - ); -@@ -818,7 +818,7 @@ - my $db=read_config($config,'db_path',''); - my $dbh; my $sth; #database and statements handlers - $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - my $st="SELECT UNCOMPRESS(COMPRESS('holacaracola'))='holacaracola'"; -@@ -841,7 +841,7 @@ - if ($version){return $version} - my $dbh; my $sth; #database and statements handlers - $dbh=open_db($db) or ( -- print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and -+ print localtime().": There was a problem opening the database $db\n" and - return 0 - ); #we open the database - $version=$dbh->get_info(18); -@@ -924,11 +924,11 @@ - if (!$only_clean){ #nothing more to do because we just should clean - if (-r $file){ - put_csv_into_db($config,$file,$table) or ( -- print localtime().": There was a problem populating the table $table with file $file\n" and -+ print localtime().": There was a problem populating the table $table with file $file: $!\n" and - return 0 - ); - }else{ -- print localtime().": WARNING no database file found, it should be $file\n"; -+ print localtime().": WARNING no database file found, it should be $file: $!\n"; - return 0; - } - } -@@ -945,11 +945,11 @@ - if (!$only_clean){ #nothing more to do because we just should clean - if (-r $file){ - put_csv_into_db($config,$file,$table) or ( -- print localtime().": There was a problem populating the table $table with file $file\n" and -+ print localtime().": There was a problem populating the table $table with file $file: $!\n" and - return 0 - ); - }else{ -- print localtime().": WARNING no working on file found, it should be $file\n"; -+ print localtime().": WARNING no working_on_dat file found, it should be $file: $!\n"; - return 0; - } - } -@@ -966,11 +966,11 @@ - if (!$only_clean){ #nothing more to do because we just should clean - if (-r $file){ - put_csv_into_db($config,$file,$table) or ( -- print localtime().": There was a problem populating the table $table with file $file\n" and -+ print localtime().": There was a problem populating the table $table with file $file: $!\n" and - return 0 - ); - }else{ -- print localtime().": WARNING no researcher file found, it should be $file\n"; -+ print localtime().": WARNING no researcher file found, it should be $file: $!\n"; - return 0; - } - } -@@ -987,11 +987,11 @@ - if (!$only_clean){ #nothing more to do because we just should clean - if (-r $file){ - put_csv_into_db($config,$file,$table) or ( -- print localtime().": There was a problem populating the table $table with file $file\n" and -+ print localtime().": There was a problem populating the table $table with file $file: $!\n" and - return 0 - ); - }else{ -- print localtime().": WARNING no marker-EST file found, it should be $file\n"; -+ print localtime().": WARNING no marker-EST file found, it should be $file: $!\n"; - return 0; - } - } -@@ -1026,11 +1026,11 @@ - my $table = 'microarray_extract'; - if (-r $file){ - put_csv_into_db($config,$file,$table) or ( -- print localtime().": There was a problem populating the table $table with file $file\n" and -+ print localtime().": There was a problem populating the table $table with file $file: $!\n" and - return 0 - ); - }else{ -- print localtime().": WARNING no extracts file found, it should be $file\n"; -+ print localtime().": WARNING no extracts file found, it should be $file: $!\n"; - return 0; - } - #loading extract mixes -@@ -1038,11 +1038,11 @@ - my $table = 'microarray_extract_mix'; - if (-r $file){ - put_csv_into_db($config,$file,$table) or ( -- print localtime().": There was a problem populating the table $table with file $file\n" and -+ print localtime().": There was a problem populating the table $table with file $file: $!\n" and - return 0 - ); - }else{ -- print localtime().": WARNING no extract mixes file found, it should be $file\n"; -+ print localtime().": WARNING no extract mixes file found, it should be $file: $!\n"; - return 0; - } - #loading the hybridizations -@@ -1050,18 +1050,18 @@ - my $table = 'microarray_hybridization'; - if (-r $file){ - put_csv_into_db($config,$file,$table) or ( -- print localtime().": There was a problem populating the table $table with file $file\n" and -+ print localtime().": There was a problem populating the table $table with file $file: $!\n" and - return 0 - ); - }else{ -- print localtime().": WARNING no hybridizations file found, it should be $file\n"; -+ print localtime().": WARNING no hybridizations file found, it should be $file: $!\n"; - return 0; - } - my $file = read_config($config,'microarray_normalized_dat',''); - my $table = 'microarray_normalized_expression'; - if (-r $file){ - open IN,"<$file" or ( -- print localtime().": Imposible to open file: $file\n" and -+ print localtime().": Imposible to open file: $file: $!\n" and - return 0 - ); - -@@ -1099,15 +1099,15 @@ - $sth->bind_param(4,$cv); - $i_hyb++; - $sth->execute or ( -- print localtime().": Unable to execute stament: $st: $DBI::errstr\n" and -- print localtime().": With line: $line\n" and -+ print localtime().": Unable to execute stament: $st\n" and -+ print localtime().": With line: $line: $DBI::errstr\n" and - return 0 - ); - } - } - close IN; - }else{ -- print localtime().": WARNING no normalized expression file found, it should be $file\n"; -+ print localtime().": WARNING no normalized expression file found, it should be $file: $!\n"; - return 0; - } - -@@ -1179,7 +1179,7 @@ - #print $contents{$table},"\n"; - create_table($db,$table,$contents{$table}) or $ok=0; - unless ($ok){ -- print localtime().": Annotation table: $table from $db can't be created\n"; -+ print localtime().": Annotation table: $table from $db can't be created: $DBI::errstr\n"; - } - } - } -@@ -1200,7 +1200,7 @@ - #if the table exist is removed - if (check_table($db,$table)) {drop_table($db,$table) or $ok=0} - unless ($ok){ -- print localtime().": Annotation table: $table from $db can't be dropped\n"; -+ print localtime().": Annotation table: $table from $db can't be dropped: $DBI::errstr\n"; - } - } - } -@@ -1220,7 +1220,7 @@ - my $db=read_config($config,'db_path',''); - - open IN,"<$file" or ( -- print localtime().": Imposible to open file $file: $!\n" and -+ print localtime().": Imposible to open file: $file: $!\n" and - return 0 - ); - -@@ -1235,10 +1235,13 @@ - return 0; - } - my $sth=prepare_st($dbh,$st) or ( -- print localtime().": Unable to prepare statement $st: $DBI::errstr\n" and -+ print localtime().": Unable to prepare statement: $st: $DBI::errstr\n" and - return 0 - ); - while ($line = <IN>){ -+ if ($line =~ /^#/) { -+ next; -+ } - chomp ($line); - $line =~ s/"//g; - my @fields=split (',',$line); -@@ -1248,8 +1251,8 @@ - $i++; - } - $sth->execute or ( -- print localtime().": Unable to execute stament $st: $DBI::errstr\n" and -- print localtime().": With line: $line\n" and -+ print localtime().": Unable to execute stament: $st\n" and -+ print localtime().": With line: $line: $DBI::errstr\n" and - return 0 - ); - } -@@ -1312,7 +1315,7 @@ - #here we read all the db structure, the table fields and contigs - my %db_structure=read_db_structure ($db_structure_file,$config); - unless (%db_structure) { -- print localtime().": There was a problem reading the database definition from file $db_structure_file: $!\n"; -+ print localtime().": There was a problem reading the database definition from file: $db_structure_file"; - return 0; - } - #the table is regenerated -@@ -1351,12 +1354,14 @@ - #Here we check that the database is reachable and has all the necesary tables - $ok=check_db_structure($db_path,%db_structure); - } -- #print_db_structure(%db_structure); -+ if (!$ok) { -+ print_db_structure(%db_structure); -+ } - return $ok; - } - - #Here we check that the database is reachable and has all the necesary tables --#this is not enough becouse fields should be checked too, so TODO -+#this is not enough because fields should be checked too, so TODO - #(although not a very important thing anyway) - sub check_db_structure($\%) { - my $db=shift; -@@ -1375,6 +1380,8 @@ - } - } - } -+ } else { -+ $ok=0; - } - if ($ok) { - print localtime().": Database structure seems ok\n"; -@@ -1422,7 +1429,7 @@ - print localtime().": Connection to the database server $db_path_no_name has failed: $DBI::errstr\n"; - return 0; - } -- #Now we check if db exists and if does is dropped -+ #Now we check if db exists and if it does it is dropped - if(db_ok($db_path)){ - #database exits, we should remove it - if(drop_db($db_path,$db_name)) { -@@ -1458,13 +1465,23 @@ - sub populate_db ($\%) { - my $db=shift; - my $tables=shift; -+ my %t = %$tables; - my $ok=1; - -+ print "populate_db called with db=$db, tables=$tables\n"; -+ #foreach my $table(keys(%t)) { -+ # print "table=$table, $t{$table}\n"; -+ #} -+ - my $table; - foreach $table(keys %$tables) { - if ($ok) { -- $ok=create_table($db,$table,${%{$tables}}{$table}); -+ $ok=create_table($db,$table,$t{$table}); # avoid Can't use string ("38/64") as a HASH ref while "strict refs" in use at /opt/est2uni/pipe_db.pm line 1477. -+ if ($ok) { - print localtime().": Table $table created\n"; -+ } else { -+ print localtime().": Table $table could not be created under dsn=$db: $DBI::errstr\n"; -+ } - } - } - return $ok; -@@ -1476,7 +1493,7 @@ - my $db=shift; - my $table_name=shift; - my $table_content=shift; #table content in sql format -- #first we check that the database is avaliable -+ #first we check that the database is available - my $ok=1; - unless (db_ok($db)) { - print localtime().": Something went wrong checking database: $db\n"; -@@ -1488,9 +1505,13 @@ - my $st="CREATE TABLE $table_name ($table_content);"; - if($ok) { - $sth=prepare_st($dbh,$st) or $ok=0; -+ } else { -+ print localtime().": There was a problem preparing a statement: $DBI::errstr\n"; - } - if ($ok) { - execute_st($sth) or $ok=0; -+ } else { -+ print localtime().": There was a problem executing a statement: $DBI::errstr\n"; - } - #print $table; - $sth->finish(); -@@ -1533,17 +1554,13 @@ - #needs a db handler - sub close_db ($) { - my $dbh=shift; -- if ($dbh){ -- $dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n"; -- } -+ if ($dbh){$dbh->disconnect();} - } - - #needs a statement handler - sub close_st ($) { - my $sth=shift; -- if ($sth){ -- $sth->finish() or print localtime().": Cannot finish execution over database: $DBI::errstr\n"; -- } -+ if ($sth){$sth->finish();} - } - - -@@ -1563,9 +1580,7 @@ - } - } - -- if ($dbh){ -- $dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n"; -- } -+ if ($dbh){$dbh->disconnect();} - return $ok; - } - -@@ -1581,9 +1596,7 @@ - else { - $ok=0; - } -- if ($dbh){ -- $dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n"; -- } -+ if ($dbh){$dbh->disconnect();} - return $ok; - } - -@@ -1594,7 +1607,7 @@ - my $ok=1; - #is the database to remove ok? - unless (db_ok($db)) { -- print localtime().": Something went wrong checking database $db: $DBI::errstr\n"; -+ print localtime().": Something went wrong checking database: $db: $DBI::errstr\n"; - $ok=0; - } - #we should open it -@@ -1619,7 +1632,7 @@ - } - } - if ($ok) {$sth->finish();} -- if ($dbh){$dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n";} -+ if ($dbh){$dbh->disconnect();} - return $ok; - } - diff --git a/sci-biology/est2uni/files/tables.sql.patch b/sci-biology/est2uni/files/tables.sql.patch deleted file mode 100644 index 3a83de8..0000000 --- a/sci-biology/est2uni/files/tables.sql.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- tables.sql.ori 2011-02-22 10:53:26.000000000 +0100 -+++ tables.sql 2011-02-22 16:15:11.000000000 +0100 -@@ -576,15 +576,15 @@ - long_name CHAR(100), - version CHAR(40), - local_blast_name CHAR(100), -- blast_program CHAR(7), -- repository CHAR(100), -- web_site CHAR(100), -- kind CHAR(40), -+ blast_program ENUM('blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'), -+ repository CHAR(255), -+ web_site CHAR(255), -+ kind ENUM('dna','pep'), - go_annot_format CHAR(40), - link_pre CHAR(200), - link_post CHAR(200), - local_hmmer_name CHAR(40), -- rec_sim_type CHAR(40), -+ rec_sim_type ENUM('', 'orthologue', 'synonymous'), - rec_sim_evalue CHAR(40), - orthologues_arabi_hack CHAR(1), - local_go_assoc_file CHAR(200), diff --git a/sci-biology/est2uni/files/tgicl_files.patch b/sci-biology/est2uni/files/tgicl_files.patch deleted file mode 100644 index ed7943a..0000000 --- a/sci-biology/est2uni/files/tgicl_files.patch +++ /dev/null @@ -1,26 +0,0 @@ ---- perl/est_clustering.pm.ori 2011-02-17 22:41:29.000000000 +0100 -+++ perl/est_clustering.pm 2011-02-17 22:42:54.000000000 +0100 -@@ -279,8 +279,11 @@ - $command="cat "; - for ($i=1; $i<=$num_micros; $i++) # a loop for every directory created by tgicl - { -+ if (-e $temp_dir.$asm_dir.$i."/".$tgicl_ace_file) -+ { - $command=$command.$temp_dir.$asm_dir.$i."/".$tgicl_ace_file." "; - } -+ } - $command.=" >".$output_ace_file; - $tgicl_success=not(system($command)); - unless ($tgicl_success) -@@ -295,8 +298,11 @@ - $command="cat "; - for ($i=1; $i<=$num_micros; $i++) # a loop for every directory created by tgicl - { -+ if (-e $temp_dir.$asm_dir.$i."/".$tgicl_fasta_file) -+ { - $command=$command.$temp_dir.$asm_dir.$i."/".$tgicl_fasta_file." "; - } -+ } - $command.=" >".$output_contig_fasta_file; - $tgicl_success=not(system($command)); - unless ($tgicl_success) diff --git a/sci-biology/est2uni/metadata.xml b/sci-biology/est2uni/metadata.xml deleted file mode 100644 index 2bc8930..0000000 --- a/sci-biology/est2uni/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> -</pkgmetadata>
