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commit baf036722d9c597adfc0802415b841643dbae31c Author: Charles Plessy <[email protected]> Date: Mon Jul 11 21:43:07 2016 +0900 Imported Upstream version 1.7~rc4 --- Bio/Root/Version.pm | 2 +- Bio/Tools/Analysis/Protein/Mitoprot.pm | 327 -------------------------- Build.PL | 7 +- DEPENDENCIES | 2 - MANIFEST | 2 - META.json | 14 +- META.yml | 13 +- examples/db/getGenBank.pl | 2 +- examples/db/get_seqs.pl | 2 +- examples/generate_random_seq.pl | 2 +- examples/searchio/psiblast_features.pl | 2 +- examples/structure/structure-io.pl | 2 +- examples/tk/hitdisplay.pl | 2 +- examples/tools/gb_to_gff.pl | 2 +- maintenance/big_split/file_classification.csv | 4 - t/Assembly/ContigSpectrum.t | 9 +- t/LocalDB/Taxonomy/sqlite.t | 40 +--- t/RemoteDB/Taxonomy.t | 1 - t/Root/IO.t | 24 +- t/Seq/PrimarySeq.t | 7 + t/Tools/Analysis/Protein/Mitoprot.t | 37 --- 21 files changed, 56 insertions(+), 447 deletions(-) diff --git a/Bio/Root/Version.pm b/Bio/Root/Version.pm index 1346148..93d65fa 100644 --- a/Bio/Root/Version.pm +++ b/Bio/Root/Version.pm @@ -36,7 +36,7 @@ variable set if it's not already. =cut -our $VERSION = '1.007000_003'; +our $VERSION = '1.007000_004'; sub import { # try to handle multiple levels of inheritance: diff --git a/Bio/Tools/Analysis/Protein/Mitoprot.pm b/Bio/Tools/Analysis/Protein/Mitoprot.pm deleted file mode 100644 index 717191d..0000000 --- a/Bio/Tools/Analysis/Protein/Mitoprot.pm +++ /dev/null @@ -1,327 +0,0 @@ -# $Id: Mitoprot.pm, -# -# BioPerl module for Bio::Tools::Analysis::Protein::Mitoprot -# Copyright Richard Adams -# -# You may distribute this module under the same terms as perl itself -# POD documentation - main docs before the code - -=head1 NAME - -Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot -server - -=head1 SYNOPSIS - - use Bio::Tools::Analysis::Protein::Mitoprot; - - use Bio::PrimarySeq; - my $seq = Bio::PrimarySeq->new - (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL', - -primary_id=>'test'); # a Bio::PrimarySeqI object - - my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new - ( -seq => $seq - ); # sequence must be >!5aa long and start with an M. - - # run Mitoprot prediction on a DNA sequence - my $mitoprot->run(); - - - die "Could not get a result" unless $mitoprot->status =~ /^COMPLETED/; - - print $mitoprot->result; # print raw prediction to STDOUT - - foreach my $feat ( $mitoprot->result('Bio::SeqFeatureI') ) { - - # do something to SeqFeature - # e.g. print as GFF - print $feat->gff_string, "\n"; - # or store within the sequence - if it is a Bio::RichSeqI - $seq->add_SeqFeature($feat); - - } - -=head1 DESCRIPTION - -This class is a wrapper around the Mitoprot web server which -calculates the probability of a sequence containing a mitochondrial -targetting peptide. See http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter -for more details. - -The results can be obtained in 3 formats: - -=over 3 - -=item 1 - -The raw text of the program output - - my $rawdata = $analysis_object->result; - -=item 2 - -An reference to a hash of scores : - - my $data_ref = $analysis_object->result('parsed'); print "predicted - export prob is $data_ref->{'export_prob'}\n"; # - -key values of returned hash are input_length, basic_aas, acidic_aas, -export_prob, charge, cleavage_site. - -=item 3 - -A Bio::SeqFeature::Generic object - - my $ft = $analysis_object->result(Bio::SeqFeatureI); - print "export prob is ", ($ft->each_tag_value('export_prob'))[0] ,"\n"; - - -This the second implentation of Bio::SimpleAnalysisI which hopefully -will make it easier to write wrappers on various services. This class -uses a web resource and therefore inherits from Bio::WebAgent. - -=back - -=head1 SEE ALSO - -L<Bio::SimpleAnalysisI>, -L<Bio::Tools::Analysis::SimpleAnalysisBase>, -L<Bio::WebAgent> - -=head1 FEEDBACK - -=head2 Mailing Lists - -User feedback is an integral part of the evolution of this and other -Bioperl modules. Send your comments and suggestions preferably to one -of the Bioperl mailing lists. Your participation is much appreciated. - - [email protected] - General discussion - http://bioperl.org/wiki/Mailing_lists - About the mailing lists - -=head2 Support - -Please direct usage questions or support issues to the mailing list: - -I<[email protected]> - -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem -with code and data examples if at all possible. - -=head2 Reporting Bugs - -Report bugs to the Bioperl bug tracking system to help us keep track -the bugs and their resolution. Bug reports can be submitted via the -web: - - https://github.com/bioperl/bioperl-live/issues - -=head1 AUTHORS - -Richard Adams, [email protected], - -=head1 APPENDIX - -The rest of the documentation details each of the object -methods. Internal methods are usually preceded with a _ - -=cut - - -# Let the code begin... - - -package Bio::Tools::Analysis::Protein::Mitoprot; -use vars qw($FLOAT); -use strict; - -use IO::String; -use Bio::SeqIO; -use HTTP::Request::Common qw(GET); -use Bio::SeqFeature::Generic; - -use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); -$FLOAT = '[+-]?\d*\.\d*'; - -my $URL = 'https://ihg.gsf.de/cgi-bin/paolo/mitofilter?'; - -my %STATUS = map { $_ => 1 } qw(CREATED COMPLETED TERMINATED_BY_ERROR); - -my $MIN_LEN = 60; #min len for protein analysis -my $ANALYSIS_NAME = "Mitoprot"; - -my $ANALYSIS_SPEC = - { - 'name' => 'Mitoprot', - 'type' => 'Protein', - 'version' => '1.0a4', - 'supplier' => 'Munich Information Center for ProteinSequences', - 'description' => 'mitochondrial sig seq prediction', - }; - -my $INPUT_SPEC = - [ - { - 'mandatory' => 'true', - 'type' => 'Bio::PrimarySeqI', - 'name' => 'seq', #value must be name of method used to set value - }, - ]; - -my $RESULT_SPEC = - { - '' => 'raw text results', # same as undef - 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', - 'all' => 'hash of results', - }; - - - -### unique to this module ## - -=head2 result - - Usage : $job->result (...) - Returns : a result created by running an analysis - Args : various - -The method returns a result of an executed job. If the job was -terminated by an error the result may contain an error message instead -of the real data. - -This implementation returns differently processed data depending on -argument: - -=over 3 - -=item undef - -Returns the raw ASCII data stream but without HTML tags - -=item 'Bio::SeqFeatureI' - -The argument string defines the type of bioperl objects returned in an -array. The objects are L<Bio::SeqFeature::Generic>. Feature primary -tag is "SigSeq". Feature tags are input_length , basic_aas, -acidic_aas, export_prob, charge, cleavage_site, method. - -=item 'parsed' - -hash references of parsed results { input_length =E<gt>, basic_aas=E<gt>, -acidic_aas=E<gt>, export_prob=E<gt>, charge=E<gt>, cleavage_site=E<gt>}. - -=back - -=cut - - -sub result { - my ($self,$value) = @_; - #make sec feat of above threshold scores # - - my @sig_pdctns; - my @fts; - - if ($value ) { - my $result = IO::String->new($self->{'_result'}); - my %results; - while (my $line = <$result>) { - #make array of all scores or threshold depending on $value - next unless $line =~ /\d/ || $line =~ /^Cle/; - if ($line =~ /^Net[^+\-\d]+ # Net, then anything except +,- or digit - ((\+|-)?\d+)/x) #then get charge with optional + or - - { - $results{'charge'} = $1; - } elsif ($line =~ /^Input[^\d]+(\d+)/ ) { - $results{'input_length'} = $1; - } elsif ($line =~ /basic[^\d]+(\d+)$/ ) { - $results{'basic_aas'} = $1; - } elsif ($line =~ /acidic[^\d]+(\d+)$/) { - $results{'acidic_aas'} = $1; - } elsif ($line =~ /^Cleavage[^\d]+(\d+)$/) { - $results{'cleavage_site'} = $1; - } elsif ($line =~ /^Cleavage/) { - $results{'cleavage_site'} = 'not predictable'; - } elsif ($line =~ /^of export[^\d]+((0|1)\.\d+)$/) { - $results{'export_prob'} = $1; - } - } - - if ($value eq 'Bio::SeqFeatureI') { - push @fts, Bio::SeqFeature::Generic->new - ( - -start => 1, - -end => ($results{'cleavage_site'} =~ - /^\d+$/)?$results{'cleavage_site'}:$self->seq->length, - -source => 'Mitoprot', - -primary => 'Region', - -tag =>{ - export_prob => $results{'export_prob'}, - charge => $results{'charge'}, - basic_aas => $results{'basic_aas'}, - acid_aas => $results{'acidic_aas'}, - region_name => 'Transit_peptide', - method => 'MitoProt', - cleavage_site => $results{'cleavage_site'}, - }, - ); - return @fts; #return Bioseqfeature array - } - ## convert parsed data into a meta array format - else { - return \%results; # hash based results ref - } - } - return $self->{'_result'}; -} - -sub _init { - my $self = shift; - $self->url($URL); - $self->{'_ANALYSIS_SPEC'} =$ANALYSIS_SPEC; - $self->{'_INPUT_SPEC'} =$INPUT_SPEC; - $self->{'_RESULT_SPEC'} =$RESULT_SPEC; - $self->{'_ANALYSIS_NAME'} =$ANALYSIS_SPEC->{'name'}; - return $self; -} - -sub _process_arguments { - #extra checking for sequence length - #mitoprot specific argument testing - my ($self, $args) = @_; - #use base checking for existence of mandatory fields - $self->SUPER::_process_arguments($args) ; - - #then check specifics - $self->throw ("1st_aa must be M") if $self->seq->subseq(1,1) !~ /M/i; - $self->throw ("sequence must be at least 15aa long") if $self->seq->length< 15; - return; -} - - - -sub _run { - #request submitted by get not by post - my $self = shift; - $self->delay(1); - $self->sleep; - - $self->status('TERMINATED_BY_ERROR'); - my $url = $self->url . "seq=" . lc($self->seq->seq) . "&seqnam="; - my $request = GET $url; - my $content = $self->request($request); - my $text = $content->content; #1st reponse - - #remove html stuff - $text =~ s/.*<PRE>(.*)<\/PRE>.*/$1/s; - $text =~ s/<[^>]+>//sg; - - $self->status('COMPLETED') if $text ne '' && $self->seq->length > $MIN_LEN; - $self->{'_result'} = $text; - -} - -1; diff --git a/Build.PL b/Build.PL index 8b5007d..af3ce3c 100644 --- a/Build.PL +++ b/Build.PL @@ -135,8 +135,6 @@ my %recommends = ( 'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ], - 'SOAP::Lite' => [ 0, 'Bibliographic queries/Bio::DB::Biblio::soap' ], - 'Sort::Naturally' => [ 0, 'Sort lexically, but sort numeral parts numerically/' @@ -167,7 +165,7 @@ my %recommends = ( 'XML::LibXML' => [ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ], - 'XML::Parser' => [ 0, 'Parsing XML/Bio::Biblio::IO::medlinexml' ], + 'XML::Parser' => [ 0, 'Parsing XML/Bio::OntologyIO::InterProParser' ], 'XML::Parser::PerlSAX' => [ 0, @@ -189,8 +187,7 @@ my %recommends = ( 'XML::Twig' => [ 0, - 'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,' - . 'Bio::DB::Biblio::eutils' + 'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez' ], 'XML::Writer' => [ diff --git a/DEPENDENCIES b/DEPENDENCIES index 9b0e39d..a74403f 100644 --- a/DEPENDENCIES +++ b/DEPENDENCIES @@ -147,7 +147,6 @@ NB: This list of packages is not authoritative. See the 'requires', |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - IO::String | | * Bio::DB::CUTG - IO::String | -| * Bio::DB::SeqHound - IO::String | | * Bio::DB::WebDBSeqI - IO::String | | * Bio::Index::Blast - IO::String | | * Bio::Index::BlastTable - IO::String | @@ -159,7 +158,6 @@ NB: This list of packages is not authoritative. See the 'requires', | * Bio::Tools::Analysis::Protein::ELM - IO::String | | * Bio::Tools::Analysis::Protein::GOR4 - IO::String | | * Bio::Tools::Analysis::Protein::HNN - IO::String | -| * Bio::Tools::Analysis::Protein::Mitoprot - IO::String | | * Bio::Tools::Analysis::Protein::NetPhos - IO::String | | * Bio::Tools::Analysis::Protein::Scansite - IO::String | | * Bio::Tools::Analysis::Protein::Sopma - IO::String | diff --git a/MANIFEST b/MANIFEST index 7b747bc..ff2facd 100644 --- a/MANIFEST +++ b/MANIFEST @@ -668,7 +668,6 @@ Bio/Tools/Analysis/Protein/Domcut.pm Bio/Tools/Analysis/Protein/ELM.pm Bio/Tools/Analysis/Protein/GOR4.pm Bio/Tools/Analysis/Protein/HNN.pm -Bio/Tools/Analysis/Protein/Mitoprot.pm Bio/Tools/Analysis/Protein/NetPhos.pm Bio/Tools/Analysis/Protein/Scansite.pm Bio/Tools/Analysis/Protein/Sopma.pm @@ -2024,7 +2023,6 @@ t/Tools/Analysis/Protein/Domcut.t t/Tools/Analysis/Protein/ELM.t t/Tools/Analysis/Protein/GOR4.t t/Tools/Analysis/Protein/HNN.t -t/Tools/Analysis/Protein/Mitoprot.t t/Tools/Analysis/Protein/NetPhos.t t/Tools/Analysis/Protein/Scansite.t t/Tools/Analysis/Protein/Sopma.t diff --git a/META.json b/META.json index b9fa154..31b3754 100644 --- a/META.json +++ b/META.json @@ -50,7 +50,6 @@ "LWP::UserAgent" : "0", "List::MoreUtils" : "0", "PostScript::TextBlock" : "0", - "SOAP::Lite" : "0", "SVG" : "2.26", "SVG::Graph" : "0.01", "Set::Scalar" : "0", @@ -231,7 +230,7 @@ "file" : "Bio/Annotation/TypeManager.pm" }, "Bio::AnnotationCollectionI" : { - "file" : "Bio/DB/HIV/HIVQueryHelper.pm" + "file" : "Bio/AnnotationCollectionI.pm" }, "Bio::AnnotationI" : { "file" : "Bio/AnnotationI.pm" @@ -871,7 +870,7 @@ "file" : "Bio/LiveSeq/Translation.pm" }, "Bio::LocatableSeq" : { - "file" : "Bio/Search/Tiling/MapTileUtils.pm" + "file" : "Bio/LocatableSeq.pm" }, "Bio::Location::Atomic" : { "file" : "Bio/Location/Atomic.pm" @@ -1364,7 +1363,7 @@ }, "Bio::Root::Build" : { "file" : "Bio/Root/Build.pm", - "version" : "1.007000_003" + "version" : "1.007000_004" }, "Bio::Root::Exception" : { "file" : "Bio/Root/Exception.pm" @@ -1395,7 +1394,7 @@ }, "Bio::Root::Version" : { "file" : "Bio/Root/Version.pm", - "version" : "1.007000_003" + "version" : "1.007000_004" }, "Bio::Search::BlastStatistics" : { "file" : "Bio/Search/BlastStatistics.pm" @@ -2111,9 +2110,6 @@ "Bio::Tools::Analysis::Protein::HNN" : { "file" : "Bio/Tools/Analysis/Protein/HNN.pm" }, - "Bio::Tools::Analysis::Protein::Mitoprot" : { - "file" : "Bio/Tools/Analysis/Protein/Mitoprot.pm" - }, "Bio::Tools::Analysis::Protein::NetPhos" : { "file" : "Bio/Tools/Analysis/Protein/NetPhos.pm" }, @@ -2511,5 +2507,5 @@ "http://dev.perl.org/licenses/"; ] }, - "version" : "1.007000_003" + "version" : "1.007000_004" } diff --git a/META.yml b/META.yml index 958c43c..deb8505 100644 --- a/META.yml +++ b/META.yml @@ -119,7 +119,7 @@ provides: Bio::Annotation::TypeManager: file: Bio/Annotation/TypeManager.pm Bio::AnnotationCollectionI: - file: Bio/DB/HIV/HIVQueryHelper.pm + file: Bio/AnnotationCollectionI.pm Bio::AnnotationI: file: Bio/AnnotationI.pm Bio::Assembly::Contig: @@ -546,7 +546,7 @@ provides: Bio::LiveSeq::Translation: file: Bio/LiveSeq/Translation.pm Bio::LocatableSeq: - file: Bio/Search/Tiling/MapTileUtils.pm + file: Bio/LocatableSeq.pm Bio::Location::Atomic: file: Bio/Location/Atomic.pm Bio::Location::AvWithinCoordPolicy: @@ -875,7 +875,7 @@ provides: file: Bio/Restriction/IO/withrefm.pm Bio::Root::Build: file: Bio/Root/Build.pm - version: 1.007000_003 + version: 1.007000_004 Bio::Root::Exception: file: Bio/Root/Exception.pm Bio::Root::HTTPget: @@ -896,7 +896,7 @@ provides: file: Bio/Root/Utilities.pm Bio::Root::Version: file: Bio/Root/Version.pm - version: 1.007000_003 + version: 1.007000_004 Bio::Search::BlastStatistics: file: Bio/Search/BlastStatistics.pm Bio::Search::BlastUtils: @@ -1373,8 +1373,6 @@ provides: file: Bio/Tools/Analysis/Protein/GOR4.pm Bio::Tools::Analysis::Protein::HNN: file: Bio/Tools/Analysis/Protein/HNN.pm - Bio::Tools::Analysis::Protein::Mitoprot: - file: Bio/Tools/Analysis/Protein/Mitoprot.pm Bio::Tools::Analysis::Protein::NetPhos: file: Bio/Tools/Analysis/Protein/NetPhos.pm Bio::Tools::Analysis::Protein::Scansite: @@ -1656,7 +1654,6 @@ recommends: LWP::UserAgent: '0' List::MoreUtils: '0' PostScript::TextBlock: '0' - SOAP::Lite: '0' SVG: '2.26' SVG::Graph: '0.01' Set::Scalar: '0' @@ -1683,4 +1680,4 @@ requires: perl: v5.6.1 resources: license: http://dev.perl.org/licenses/ -version: 1.007000_003 +version: 1.007000_004 diff --git a/examples/db/getGenBank.pl b/examples/db/getGenBank.pl index 01ea6b7..b2621d4 100755 --- a/examples/db/getGenBank.pl +++ b/examples/db/getGenBank.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # # How to retrieve GenBank entries over the Web # diff --git a/examples/db/get_seqs.pl b/examples/db/get_seqs.pl index cf2df29..29c1cf6 100755 --- a/examples/db/get_seqs.pl +++ b/examples/db/get_seqs.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl use strict; use vars qw($USAGE); use Carp; diff --git a/examples/generate_random_seq.pl b/examples/generate_random_seq.pl index 2849fac..9eb44bf 100755 --- a/examples/generate_random_seq.pl +++ b/examples/generate_random_seq.pl @@ -1,4 +1,4 @@ -#!/bin/perl +#!/usr/bin/perl use strict; use vars qw($USAGE); diff --git a/examples/searchio/psiblast_features.pl b/examples/searchio/psiblast_features.pl index e6fbf0c..e98a362 100755 --- a/examples/searchio/psiblast_features.pl +++ b/examples/searchio/psiblast_features.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # Example usage of a SearchIO::psiblast parser of traditional format Blast # and PSI-Blast reports. diff --git a/examples/structure/structure-io.pl b/examples/structure/structure-io.pl index 8cec9b4..37d6fee 100755 --- a/examples/structure/structure-io.pl +++ b/examples/structure/structure-io.pl @@ -1,4 +1,4 @@ -#!/bin/perl +#!/usr/bin/perl # Getting Entry, Chain, Residue, and Atom objects given a PDB file use Bio::Structure::IO; diff --git a/examples/tk/hitdisplay.pl b/examples/tk/hitdisplay.pl index 97a41ad..e808a58 100755 --- a/examples/tk/hitdisplay.pl +++ b/examples/tk/hitdisplay.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # # PROGRAM : hitdisplay.pl # PURPOSE : Demonstrate Bio::Tk::HitDisplay diff --git a/examples/tools/gb_to_gff.pl b/examples/tools/gb_to_gff.pl index bacf12a..eee2ec0 100755 --- a/examples/tools/gb_to_gff.pl +++ b/examples/tools/gb_to_gff.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl use strict; use Bio::Tools::GFF; diff --git a/maintenance/big_split/file_classification.csv b/maintenance/big_split/file_classification.csv index 03bd4bb..e46fe2b 100644 --- a/maintenance/big_split/file_classification.csv +++ b/maintenance/big_split/file_classification.csv @@ -526,7 +526,6 @@ "Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedTableFeatureI.pm" "AcePerl","Bio/DB/Ace.pm" ,"Bio/DB/GenPept.pm" -,"Bio/DB/SeqHound.pm" ,"Bio/DB/Flat/BDB.pm" ,"Bio/DB/Flat/BinarySearch.pm" ,"Bio/DB/Flat/BDB/swiss.pm" @@ -833,7 +832,6 @@ ,"Bio/Tools/Analysis/SimpleAnalysisBase.pm" ,"Bio/Tools/Analysis/DNA/ESEfinder.pm" ,"Bio/Tools/Analysis/Protein/Domcut.pm" -,"Bio/Tools/Analysis/Protein/Mitoprot.pm" ,"Bio/Tools/Analysis/Protein/Sopma.pm" ,"Bio/Tools/Analysis/Protein/NetPhos.pm" ,"Bio/Tools/Analysis/Protein/Scansite.pm" @@ -2060,7 +2058,6 @@ ,"t/RemoteDB/EUtilities.t" ,"t/RemoteDB/EntrezGene.t" ,"t/RemoteDB/BioFetch.t" -,"t/RemoteDB/SeqHound.t" ,"t/RemoteDB/CUTG.t" ,"t/RemoteDB/Query/GenBank.t" ,"t/RemoteDB/SeqVersion.t" @@ -2161,7 +2158,6 @@ ,"t/Tools/EUtilities/egquery.t" ,"t/Tools/Analysis/DNA/ESEfinder.t" ,"t/Tools/Analysis/Protein/Sopma.t" -,"t/Tools/Analysis/Protein/Mitoprot.t" ,"t/Tools/Analysis/Protein/GOR4.t" ,"t/Tools/Analysis/Protein/Scansite.t" ,"t/Tools/Analysis/Protein/ELM.t" diff --git a/t/Assembly/ContigSpectrum.t b/t/Assembly/ContigSpectrum.t index 760e058..910d441 100644 --- a/t/Assembly/ContigSpectrum.t +++ b/t/Assembly/ContigSpectrum.t @@ -313,9 +313,12 @@ SKIP: { float_is $large_csp->avg_seq_len, 100; is $large_csp->nof_overlaps, 26; is $large_csp->min_overlap, 54; - # operation returns sometimes 88.76923... and sometimes 88.80769... - ok $large_csp->avg_overlap >= 88.7692; - ok $large_csp->avg_overlap <= 88.8077; + + # Stochastic test results: + # Operation returns sometimes 88.76923... and sometimes 88.80769... + + cmp_ok($large_csp->avg_overlap, '>=', 85); + cmp_ok($large_csp->avg_overlap, '<=', 95); float_is $large_csp->min_identity, 33.3333; cmp_ok($large_csp->avg_identity, '>=', 70, $large_csp->avg_identity); cmp_ok($large_csp->avg_identity, '<=', 80, $large_csp->avg_identity); diff --git a/t/LocalDB/Taxonomy/sqlite.t b/t/LocalDB/Taxonomy/sqlite.t index 30d8226..ca02db2 100644 --- a/t/LocalDB/Taxonomy/sqlite.t +++ b/t/LocalDB/Taxonomy/sqlite.t @@ -7,10 +7,9 @@ BEGIN { use lib '.'; use Bio::Root::Test; - #test_begin( - # - # -requires_modules => [qw(DBI DBD::SQLite )] - #); + test_begin( + -requires_modules => [qw(DB_File DBI DBD::SQLite )] + ); use_ok('Bio::DB::Taxonomy'); use_ok('Bio::Tree::Tree'); @@ -29,39 +28,6 @@ ok my $db_flatfile = Bio::DB::Taxonomy->new( isa_ok $db_flatfile, 'Bio::DB::Taxonomy::sqlite'; isa_ok $db_flatfile, 'Bio::DB::Taxonomy'; -# By not specifying a '-directory' argument, index files go to a temporary -# folder ($Bio::Root::IO::TEMPDIR, such as 'C:\Users\USER\AppData\Local\Temp'), -# and are implied to be temporary. So test the ability of flatfile->DESTROY to -# remove the temporary index files at object destruction (this also affects files -# in "test_output_dir()", since the folder is created inside the temporary folder) -#no warnings qw(once); # silence 'Name "$Bio::Root::IO::TEMPDIR" used only once' -# -#is $db_flatfile->{index_directory}, $Bio::Root::IO::TEMPDIR, 'removal of temporary index files: no -directory'; - -#$db_flatfile->DESTROY; -#ok not -e ($db_flatfile->{index_directory} . '/id2names'); -#ok not -e ($db_flatfile->{index_directory} . '/names2id'); -#ok not -e ($db_flatfile->{index_directory} . '/nodes'); -#ok not -e ($db_flatfile->{index_directory} . '/parents'); - -## Test removal of temporary index files from test_output_dir folder -## (since test_output_dir() =~ m/^$Bio::Root::IO::TEMPDIR/) -#ok $db_flatfile = Bio::DB::Taxonomy->new( -# -source => 'flatfile', -# -directory => $temp_dir, -# -nodesfile => test_input_file('taxdump', 'nodes.dmp'), -# -namesfile => test_input_file('taxdump', 'names.dmp'), -# -force => 1, -#); -#is $db_flatfile->{index_directory}, $temp_dir, 'removal of temporary index files: test_output_dir()'; -#$db_flatfile->DESTROY; -#ok not -e ($db_flatfile->{index_directory} . '/id2names'); -#ok not -e ($db_flatfile->{index_directory} . '/names2id'); -#ok not -e ($db_flatfile->{index_directory} . '/nodes'); -#ok not -e ($db_flatfile->{index_directory} . '/parents'); -# -# Generate the object (and the files) again for the remaining tests - ok my $db = Bio::DB::Taxonomy->new( -source => 'sqlite', -directory => $temp_dir, diff --git a/t/RemoteDB/Taxonomy.t b/t/RemoteDB/Taxonomy.t index bf58bff..f7b5951 100644 --- a/t/RemoteDB/Taxonomy.t +++ b/t/RemoteDB/Taxonomy.t @@ -182,7 +182,6 @@ for my $db ($db_entrez, $db_flatfile) { } else { # note the locally cached flatfile is out-of-date, but technically # correct for testing purposes - diag(join(",", @ids)); ok grep { $_ == 266791 } @ids; ok grep { $_ == 5533 } @ids; } diff --git a/t/Root/IO.t b/t/Root/IO.t index 23dfe4f..4e95caa 100644 --- a/t/Root/IO.t +++ b/t/Root/IO.t @@ -284,22 +284,38 @@ SKIP: { $expected = "DEFINITION Desmognathus quadramaculatus 12S ribosomal RNA gene, partial\n"; is $unix_rio->_readline, $expected; - is $win_rio->_readline , $expected; + TODO: { + local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/". + "Windows line endings: #"; + is $win_rio->_readline , $expected; + }; is $mac_rio->_readline , $expected; $expected = " sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA\n"; is $unix_rio->_readline, $expected; - is $win_rio->_readline , $expected; + TODO: { + local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/". + "Windows line endings: #"; + is $win_rio->_readline , $expected; + }; is $mac_rio->_readline , $expected; $expected = " gene, partial sequence, mitochondrial genes for mitochondrial RNAs.\n"; is $unix_rio->_readline, $expected; - is $win_rio->_readline , $expected; + TODO: { + local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/". + "Windows line endings: #"; + is $win_rio->_readline , $expected; + }; is $mac_rio->_readline , $expected; $expected = "ACCESSION U71225\n"; is $unix_rio->_readline, $expected; - is $win_rio->_readline , $expected; + TODO: { + local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/". + "Windows line endings: #"; + is $win_rio->_readline , $expected; + }; is $mac_rio->_readline , $expected; # $HAS_EOL ignores -raw diff --git a/t/Seq/PrimarySeq.t b/t/Seq/PrimarySeq.t index 93d430e..22fed4a 100644 --- a/t/Seq/PrimarySeq.t +++ b/t/Seq/PrimarySeq.t @@ -291,14 +291,21 @@ is $seq->seq('TTGGTGGCG?CAACT'), 'TTGGTGGCG?CAACT'; # frame 1, frame 0 start < frame 1 start, then should return the frame # 0 ORF per the pod ('the first orf') even if frame 1 stop < frame 0 stop +# Turn off warnings for a few tests +my $verbosity = $seq->verbose(); +$seq->verbose(-1); + $seq->seq('ATGAATGTAAATAA'); $aa = $seq->translate( -orf => 1 ); my $aa0 = $seq->translate(-frame => 0); + is $aa->seq, $aa0->seq, "frame 0 start, frame 1 stop < frame 0 stop"; $seq->seq('AAATGAATGTAAATAA'); $aa = $seq->translate( -orf => 1, -frame=>1 ); my $aa2 = $seq->translate(-frame => 2); is $aa->seq, $aa2->seq, "frame 1 start, frame 2 stop < frame 1 stop"; +# Turn 'em back on! +$seq->verbose($verbosity); # test for some aliases $seq = Bio::PrimarySeq->new( diff --git a/t/Tools/Analysis/Protein/Mitoprot.t b/t/Tools/Analysis/Protein/Mitoprot.t deleted file mode 100644 index 5fe60e8..0000000 --- a/t/Tools/Analysis/Protein/Mitoprot.t +++ /dev/null @@ -1,37 +0,0 @@ -# -*-Perl-*- Test Harness script for Bioperl -# $Id$ - -use strict; - -BEGIN { - use lib '.'; - use Bio::Root::Test; - - test_begin(-tests => 10, - -requires_modules => [qw(IO::String LWP::UserAgent)], - -requires_networking => 1); - - use_ok 'Bio::Tools::Analysis::Protein::Mitoprot'; - use_ok 'Bio::PrimarySeq'; - use_ok 'Bio::WebAgent'; -} - -my $verbose = test_debug(); - -ok my $tool = Bio::WebAgent->new(-verbose =>$verbose); - -my $seq = Bio::PrimarySeq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDSFFGSDFDGDS' - . 'DFGSDFGSDGDFGSDFGDSFGDGFSDRSRQDQRS', - -display_id => 'test2'); - -ok $tool = Bio::Tools::Analysis::Protein::Mitoprot->new( -seq=>$seq); -SKIP: { - ok $tool->run(); - skip( 'Server terminated with an error, skipping tests', 4 ) - if ( $tool->status eq 'TERMINATED_BY_ERROR' - or $tool->result =~ /Can't connect to/ ); - ok my $raw = $tool->result(''); - ok my $parsed = $tool->result('parsed'); - is ($parsed->{'charge'}, -13); - ok my @res = $tool->result('Bio::SeqFeatureI'); -} -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bioperl.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
