[med-svn] r12358 - in trunk/packages/conservation-code/trunk/debian: . patches

Wed Oct 10 13:43:21 UTC 2012

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 <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Laszlo Kajan <lkajan at rostlab.org>
-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 <lkajan at rostlab.org>
-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


