Author: lkajan-guest Date: 2012-10-10 13:43:21 +0000 (Wed, 10 Oct 2012) New Revision: 12358
Added: trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod Removed: trunk/packages/conservation-code/trunk/debian/patches/manpage Modified: trunk/packages/conservation-code/trunk/debian/ trunk/packages/conservation-code/trunk/debian/control trunk/packages/conservation-code/trunk/debian/manpages trunk/packages/conservation-code/trunk/debian/patches/series trunk/packages/conservation-code/trunk/debian/rules Log: moved man page POD to debian dir from patch file; removed DM-Upload-Allowed field from d/control Property changes on: trunk/packages/conservation-code/trunk/debian ___________________________________________________________________ Added: svn:ignore + score_conservation.1 Modified: trunk/packages/conservation-code/trunk/debian/control =================================================================== --- trunk/packages/conservation-code/trunk/debian/control 2012-10-09 21:03:23 UTC (rev 12357) +++ trunk/packages/conservation-code/trunk/debian/control 2012-10-10 13:43:21 UTC (rev 12358) @@ -3,12 +3,11 @@ Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Laszlo Kajan <[email protected]> -Build-Depends: debhelper (>= 8.0.0) +Build-Depends: debhelper (>= 8.0.0), python Standards-Version: 3.9.4 Homepage: http://compbio.cs.princeton.edu/conservation/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/conservation-code/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/conservation-code/trunk/ -DM-Upload-Allowed: yes Package: conservation-code Architecture: all Modified: trunk/packages/conservation-code/trunk/debian/manpages =================================================================== --- trunk/packages/conservation-code/trunk/debian/manpages 2012-10-09 21:03:23 UTC (rev 12357) +++ trunk/packages/conservation-code/trunk/debian/manpages 2012-10-10 13:43:21 UTC (rev 12358) @@ -1 +1 @@ -score_conservation.1 +debian/score_conservation.1 Deleted: trunk/packages/conservation-code/trunk/debian/patches/manpage =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/manpage 2012-10-09 21:03:23 UTC (rev 12357) +++ trunk/packages/conservation-code/trunk/debian/patches/manpage 2012-10-10 13:43:21 UTC (rev 12358) @@ -1,158 +0,0 @@ -Author: Laszlo Kajan <[email protected]> -Description: man page for score_conservation(1) -Forwarded: no ---- /dev/null -+++ b/score_conservation.1.pod -@@ -0,0 +1,152 @@ -+=pod -+ -+=head1 NAME -+ -+score_conservation - score protein sequence conservation -+ -+=head1 SYNOPSIS -+ -+score_conservation [options] ALIGNFILE -+ -+=head1 DESCRIPTION -+ -+Score protein sequence conservation in B<ALIGNFILE>. B<ALIGNFILE> must be in FASTA or CLUSTAL format. -+ -+The following conservation scoring methods are implemented: -+ * sum of pairs -+ * weighted sum of pairs -+ * Shannon entropy -+ * Shannon entropy with property groupings (Mirny and Shakhnovich 1995, -+ Valdar and Thornton 2001) -+ * relative entropy with property groupings (Williamson 1995) -+ * von Neumann entropy (Caffrey et al 2004) -+ * relative entropy (Samudrala and Wang 2006) -+ * Jensen-Shannon divergence (Capra and Singh 2007) -+ -+A window-based extension that incorporates the estimated conservation of -+sequentially adjacent residues into the score for each column is also given. -+This window approach can be applied to any of the conservation scoring -+methods. -+ -+With default parameters score_conservation(1) computes the conservation scores for the alignment using the -+Jensen-Shannon divergence and a window B<-w> of I<3>. -+ -+The sequence-specific output can be used as the conservation input for -+concavity. -+ -+Conservation is highly predictive in identifying catalytic sites and -+residues near bound ligands. -+ -+=head1 REFERENCES -+ -+=over -+ -+=item Capra JA and Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics, 23(15):1875-82, 2007. -+ -+=back -+ -+=head1 OPTIONS -+ -+=over -+ -+=item -a [NAME] -+ -+Reference sequence. Print scores in reference to the named sequence (ignoring gaps). Default prints the entire column. -+ -+=item -b [0-1] -+ -+Lambda for window heuristic linear combination. Default=I<.5>. -+ -+Equation: -+ -+C<score = (1 - lambda) * average_score_over_window_around_middle + lambda * score_of_middle> -+ -+=item -d [FILE] -+ -+Background distribution file, e.g. F<distributions/swissprot.distribution>. Default=built-in BLOSUM62. -+ -+=item -g [0-1)] -+ -+Gap cutoff. Do not score columns that contain more than gap cutoff fraction gaps. Default=I<.3>. -+ -+=item -h -+ -+Print help. -+ -+=item -l [true|false] -+ -+Use sequence weighting. Default=I<true>. -+ -+=item -m [FILE] -+ -+Similarity matrix file, e.g. F<matrix/blosum62.bla> or .qij. Default=F<matrix/blosum62.bla>. -+ -+Some methods, e.g. I<js_divergence>, do not use this. -+ -+=item -n [true|false] -+ -+Normalize scores. Print the z-score (over the alignment) of each column raw score. Default=I<false>. -+ -+=item -o FILE -+ -+Output file. Default: standard output stream. -+ -+=item -p [true|false] -+ -+Use gap penalty. Lower the score of columns that contain gaps, proportionally to the sum weight of the gapped sequences. Default=I<true>. -+ -+=item -s [METHOD] -+ -+Conservation estimation method, one of I<shannon_entropy property_entropy property_relative_entropy vn_entropy relative_entropy js_divergence sum_of_pairs>. Default=I<js_divergence>. -+ -+=item -w [0-INT] -+ -+Window size. Number of residues on either side included in the window. Default=I<3>. -+ -+=back -+ -+=head1 EXAMPLES -+ -+Note: you may have to copy and uncompress the example data files before running the following examples. -+ -+=over -+ -+=item Compute conservation scores for the alignment using the Jensen-Shannon divergence with default settings and print out the scores: -+ -+ score_conservation __docdir__/examples/2plc__hssp-filtered.aln -+ -+=item Score an alignment using Jensen-Shannon divergence, a window of size 3 (on either side of the residue), and the swissprot background distribution: -+ -+ score_conservation -s js_divergence -w 3 -d \ -+ __pkgdatadir__/distributions/swissprot.distribution \ -+ __docdir__/examples/2plc__hssp-filtered.aln -+ -+=back -+ -+=head1 FILES -+ -+=over -+ -+=item Distributions -+ -+F<__pkgdatadir__/distributions> -+ -+=item Matrices -+ -+F<__pkgdatadir__/matrix> -+ -+=back -+ -+=head1 SEE ALSO -+ -+=over -+ -+=item Homepage L<http://compbio.cs.princeton.edu/conservation/> -+ -+=item Publication L<http://bioinformatics.oxfordjournals.org/cgi/content/full/23/15/1875> -+ -+=item concavity(1) -+ -+=back -+ -+=cut Modified: trunk/packages/conservation-code/trunk/debian/patches/series =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/series 2012-10-09 21:03:23 UTC (rev 12357) +++ trunk/packages/conservation-code/trunk/debian/patches/series 2012-10-10 13:43:21 UTC (rev 12358) @@ -1,3 +1,2 @@ examples -manpage score_conservation Modified: trunk/packages/conservation-code/trunk/debian/rules =================================================================== --- trunk/packages/conservation-code/trunk/debian/rules 2012-10-09 21:03:23 UTC (rev 12357) +++ trunk/packages/conservation-code/trunk/debian/rules 2012-10-10 13:43:21 UTC (rev 12358) @@ -4,7 +4,7 @@ PACKAGE:=$(shell dpkg-parsechangelog --format rfc822|sed --posix -n -e 's/^Source: \(.*\)/\1/p;') VERSION:=$(shell dpkg-parsechangelog --format rfc822|sed --posix -n -e 's/^Version: \([0-9.]*\).*/\1/p;') -MANS=score_conservation.1 +MANS=debian/score_conservation.1 prefix?=/usr datarootdir:=${prefix}/share Added: trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod =================================================================== --- trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod (rev 0) +++ trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod 2012-10-10 13:43:21 UTC (rev 12358) @@ -0,0 +1,152 @@ +=pod + +=head1 NAME + +score_conservation - score protein sequence conservation + +=head1 SYNOPSIS + +score_conservation [options] ALIGNFILE + +=head1 DESCRIPTION + +Score protein sequence conservation in B<ALIGNFILE>. B<ALIGNFILE> must be in FASTA or CLUSTAL format. + +The following conservation scoring methods are implemented: + * sum of pairs + * weighted sum of pairs + * Shannon entropy + * Shannon entropy with property groupings (Mirny and Shakhnovich 1995, + Valdar and Thornton 2001) + * relative entropy with property groupings (Williamson 1995) + * von Neumann entropy (Caffrey et al 2004) + * relative entropy (Samudrala and Wang 2006) + * Jensen-Shannon divergence (Capra and Singh 2007) + +A window-based extension that incorporates the estimated conservation of +sequentially adjacent residues into the score for each column is also given. +This window approach can be applied to any of the conservation scoring +methods. + +With default parameters score_conservation(1) computes the conservation scores for the alignment using the +Jensen-Shannon divergence and a window B<-w> of I<3>. + +The sequence-specific output can be used as the conservation input for +concavity. + +Conservation is highly predictive in identifying catalytic sites and +residues near bound ligands. + +=head1 REFERENCES + +=over + +=item Capra JA and Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics, 23(15):1875-82, 2007. + +=back + +=head1 OPTIONS + +=over + +=item -a [NAME] + +Reference sequence. Print scores in reference to the named sequence (ignoring gaps). Default prints the entire column. + +=item -b [0-1] + +Lambda for window heuristic linear combination. Default=I<.5>. + +Equation: + +C<score = (1 - lambda) * average_score_over_window_around_middle + lambda * score_of_middle> + +=item -d [FILE] + +Background distribution file, e.g. F<distributions/swissprot.distribution>. Default=built-in BLOSUM62. + +=item -g [0-1)] + +Gap cutoff. Do not score columns that contain more than gap cutoff fraction gaps. Default=I<.3>. + +=item -h + +Print help. + +=item -l [true|false] + +Use sequence weighting. Default=I<true>. + +=item -m [FILE] + +Similarity matrix file, e.g. F<matrix/blosum62.bla> or .qij. Default=F<matrix/blosum62.bla>. + +Some methods, e.g. I<js_divergence>, do not use this. + +=item -n [true|false] + +Normalize scores. Print the z-score (over the alignment) of each column raw score. Default=I<false>. + +=item -o FILE + +Output file. Default: standard output stream. + +=item -p [true|false] + +Use gap penalty. Lower the score of columns that contain gaps, proportionally to the sum weight of the gapped sequences. Default=I<true>. + +=item -s [METHOD] + +Conservation estimation method, one of I<shannon_entropy property_entropy property_relative_entropy vn_entropy relative_entropy js_divergence sum_of_pairs>. Default=I<js_divergence>. + +=item -w [0-INT] + +Window size. Number of residues on either side included in the window. Default=I<3>. + +=back + +=head1 EXAMPLES + +Note: you may have to copy and uncompress the example data files before running the following examples. + +=over + +=item Compute conservation scores for the alignment using the Jensen-Shannon divergence with default settings and print out the scores: + + score_conservation __docdir__/examples/2plc__hssp-filtered.aln + +=item Score an alignment using Jensen-Shannon divergence, a window of size 3 (on either side of the residue), and the swissprot background distribution: + + score_conservation -s js_divergence -w 3 -d \ + __pkgdatadir__/distributions/swissprot.distribution \ + __docdir__/examples/2plc__hssp-filtered.aln + +=back + +=head1 FILES + +=over + +=item Distributions + +F<__pkgdatadir__/distributions> + +=item Matrices + +F<__pkgdatadir__/matrix> + +=back + +=head1 SEE ALSO + +=over + +=item Homepage L<http://compbio.cs.princeton.edu/conservation/> + +=item Publication L<http://bioinformatics.oxfordjournals.org/cgi/content/full/23/15/1875> + +=item concavity(1) + +=back + +=cut _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
