Author: lkajan-guest Date: 2012-10-11 11:32:24 +0000 (Thu, 11 Oct 2012) New Revision: 12385
Added: trunk/packages/conservation-code/trunk/debian/patches/default_matrix_path trunk/packages/conservation-code/trunk/debian/patches/numpy.numarray trunk/packages/conservation-code/trunk/debian/patches/optimize_loop trunk/packages/conservation-code/trunk/debian/patches/script_name Removed: trunk/packages/conservation-code/trunk/debian/patches/score_conservation Modified: trunk/packages/conservation-code/trunk/debian/control trunk/packages/conservation-code/trunk/debian/patches/series trunk/packages/conservation-code/trunk/debian/rules Log: applied Jakub Wilks advice Modified: trunk/packages/conservation-code/trunk/debian/control =================================================================== --- trunk/packages/conservation-code/trunk/debian/control 2012-10-11 10:57:56 UTC (rev 12384) +++ trunk/packages/conservation-code/trunk/debian/control 2012-10-11 11:32:24 UTC (rev 12385) @@ -3,7 +3,7 @@ Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Laszlo Kajan <[email protected]> -Build-Depends: debhelper (>= 8.0.0), python +Build-Depends: debhelper (>= 8.0.0), perl, python (>= 2.6.6-3~) 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/ Added: trunk/packages/conservation-code/trunk/debian/patches/default_matrix_path =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/default_matrix_path (rev 0) +++ trunk/packages/conservation-code/trunk/debian/patches/default_matrix_path 2012-10-11 11:32:24 UTC (rev 12385) @@ -0,0 +1,14 @@ +Author: Laszlo Kajan <[email protected]> +Description: correct path to packaged default matrix file +Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-October/017448.html +--- a/score_conservation.py ++++ b/score_conservation.py +@@ -718,7 +718,7 @@ + window_size = 3 # 0 = no window + win_lam = .5 # for window method linear combination + outfile_name = "" +-s_matrix_file = "matrix/blosum62.bla" ++s_matrix_file = "/usr/share/conservation-code/matrix/blosum62.bla" + bg_distribution = blosum_background_distr[:] + scoring_function = js_divergence + use_seq_weights = True Added: trunk/packages/conservation-code/trunk/debian/patches/numpy.numarray =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/numpy.numarray (rev 0) +++ trunk/packages/conservation-code/trunk/debian/patches/numpy.numarray 2012-10-11 11:32:24 UTC (rev 12385) @@ -0,0 +1,14 @@ +Author: Laszlo Kajan <[email protected]> +Description: fix import of numarray from numpy.numarray +Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-October/017448.html +--- a/score_conservation.py ++++ b/score_conservation.py +@@ -790,7 +790,7 @@ + if arg == 'shannon_entropy': scoring_function = shannon_entropy + elif arg == 'property_entropy': scoring_function = property_entropy + elif arg == 'property_relative_entropy': scoring_function = property_relative_entropy +- elif arg == 'vn_entropy': scoring_function = vn_entropy; from numarray import *; import numarray.linear_algebra as la ++ elif arg == 'vn_entropy': scoring_function = vn_entropy; from numpy.numarray import *; import numpy.numarray.linear_algebra as la + + elif arg == 'relative_entropy': scoring_function = relative_entropy + elif arg == 'js_divergence': scoring_function = js_divergence Added: trunk/packages/conservation-code/trunk/debian/patches/optimize_loop =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/optimize_loop (rev 0) +++ trunk/packages/conservation-code/trunk/debian/patches/optimize_loop 2012-10-11 11:32:24 UTC (rev 12385) @@ -0,0 +1,16 @@ +Author: Laszlo Kajan <[email protected]> +Description: move code outside of loop +Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-October/017448.html +--- a/score_conservation.py ++++ b/score_conservation.py +@@ -136,8 +136,9 @@ + + aa_num += 1 + ++ freqsum = (sum(seq_weights) + len(amino_acids) * pc_amount) + for j in range(len(freq_counts)): +- freq_counts[j] = freq_counts[j] / (sum(seq_weights) + len(amino_acids) * pc_amount) ++ freq_counts[j] = freq_counts[j] / freqsum + + return freq_counts + Deleted: trunk/packages/conservation-code/trunk/debian/patches/score_conservation =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/score_conservation 2012-10-11 10:57:56 UTC (rev 12384) +++ trunk/packages/conservation-code/trunk/debian/patches/score_conservation 2012-10-11 11:32:24 UTC (rev 12385) @@ -1,49 +0,0 @@ -Author: Laszlo Kajan <[email protected]> -Description: fixes to executable -Forwarded: no ---- a/score_conservation -+++ b/score_conservation -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/python - - ################################################################################ - # score_conservation.py - Copyright Tony Capra 2007 - Last Update: 03/09/11 -@@ -98,7 +98,7 @@ - - - def usage(): -- print """\nUSAGE:\npython score_conservation.py [options] alignfile\n\t -alignfile must be in fasta or clustal format.\n\nOPTIONS:\n\t -+ print """\nUSAGE:\nscore_conservation [options] alignfile\n\t -alignfile must be in fasta or clustal format.\n\nOPTIONS:\n\t - -a\treference sequence. Print scores in reference to a specific sequence (ignoring gaps). Default prints the entire column. [sequence name]\n\t - -b\tlambda for window heuristic linear combination. Default=.5 [real in [0,1]]\n - -d\tbackground distribution file, e.g., swissprot.distribution. Default=BLOSUM62 background [filename]\n\t -@@ -136,8 +136,9 @@ - - aa_num += 1 - -+ freqsum = (sum(seq_weights) + len(amino_acids) * pc_amount) - for j in range(len(freq_counts)): -- freq_counts[j] = freq_counts[j] / (sum(seq_weights) + len(amino_acids) * pc_amount) -+ freq_counts[j] = freq_counts[j] / freqsum - - return freq_counts - -@@ -718,7 +719,7 @@ - window_size = 3 # 0 = no window - win_lam = .5 # for window method linear combination - outfile_name = "" --s_matrix_file = "matrix/blosum62.bla" -+s_matrix_file = "/usr/share/conservation-code/matrix/blosum62.bla" - bg_distribution = blosum_background_distr[:] - scoring_function = js_divergence - use_seq_weights = True -@@ -790,7 +791,7 @@ - if arg == 'shannon_entropy': scoring_function = shannon_entropy - elif arg == 'property_entropy': scoring_function = property_entropy - elif arg == 'property_relative_entropy': scoring_function = property_relative_entropy -- elif arg == 'vn_entropy': scoring_function = vn_entropy; from numarray import *; import numarray.linear_algebra as la -+ elif arg == 'vn_entropy': scoring_function = vn_entropy; from numpy.numarray import *; import numpy.numarray.linear_algebra as la - - elif arg == 'relative_entropy': scoring_function = relative_entropy - elif arg == 'js_divergence': scoring_function = js_divergence Added: trunk/packages/conservation-code/trunk/debian/patches/script_name =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/script_name (rev 0) +++ trunk/packages/conservation-code/trunk/debian/patches/script_name 2012-10-11 11:32:24 UTC (rev 12385) @@ -0,0 +1,22 @@ +Author: Laszlo Kajan <[email protected]> +Description: change interpreter and remove extension from script + Policy §1.4.2 Interpreter Location: 'The preferred specification for the Python interpreter is /usr/bin/python'. + Policy §10.4 Scripts: 'the script name should not include an extension'. +Forwarded: no +--- a/score_conservation.py ++++ b/score_conservation.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + ################################################################################ + # score_conservation.py - Copyright Tony Capra 2007 - Last Update: 03/09/11 +@@ -98,7 +98,7 @@ + + + def usage(): +- print """\nUSAGE:\npython score_conservation.py [options] alignfile\n\t -alignfile must be in fasta or clustal format.\n\nOPTIONS:\n\t ++ print """\nUSAGE:\nscore_conservation [options] alignfile\n\t -alignfile must be in fasta or clustal format.\n\nOPTIONS:\n\t + -a\treference sequence. Print scores in reference to a specific sequence (ignoring gaps). Default prints the entire column. [sequence name]\n\t + -b\tlambda for window heuristic linear combination. Default=.5 [real in [0,1]]\n + -d\tbackground distribution file, e.g., swissprot.distribution. Default=BLOSUM62 background [filename]\n\t Modified: trunk/packages/conservation-code/trunk/debian/patches/series =================================================================== --- trunk/packages/conservation-code/trunk/debian/patches/series 2012-10-11 10:57:56 UTC (rev 12384) +++ trunk/packages/conservation-code/trunk/debian/patches/series 2012-10-11 11:32:24 UTC (rev 12385) @@ -1,2 +1,5 @@ examples -score_conservation +script_name +numpy.numarray +default_matrix_path +optimize_loop Modified: trunk/packages/conservation-code/trunk/debian/rules =================================================================== --- trunk/packages/conservation-code/trunk/debian/rules 2012-10-11 10:57:56 UTC (rev 12384) +++ trunk/packages/conservation-code/trunk/debian/rules 2012-10-11 11:32:24 UTC (rev 12385) @@ -4,6 +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;') +SCRIPTS=score_conservation MANS=debian/score_conservation.1 prefix?=/usr @@ -11,30 +12,19 @@ docdir:=${datarootdir}/doc/${PACKAGE} pkgdatadir:=${datarootdir}/${PACKAGE} +# Policy §4.9 says that the get-orig-source target 'may be invoked in any directory'. So we do not use variables set from dpkg-parsechangelog. .PHONY: get-orig-source get-orig-source: set -e; \ - if ! which xz; then \ - echo "Could not find 'xz' tool for compression. Please apt-get install xz-utils." ; \ - exit ; \ - fi ; \ t=$$(mktemp -d) || exit 1; \ trap "rm -rf -- '$$t'" EXIT; \ - pwd; \ - o=conservation-code_$(VERSION).orig.tar; \ - wget -O $$t/$${o}.gz http://compbio.cs.princeton.edu/conservation/conservation_code.tar.gz; \ ( cd "$$t"; \ - gunzip *.tar.gz; \ - tar --owner=root --group=root --mode=a+rX --delete -f *.tar --wildcards '*/.*'; \ - tar --owner=root --group=root --mode=a+rX --extract -f *.tar; rm -f *.tar; \ - mv conservation_code/score_conservation.py conservation_code/score_conservation; \ - tar --owner=root --group=root --mode=a+rX --create -f $$o conservation_code; \ - xz --best *.tar; \ + wget -O conservation-code_20110309.0.orig.tar.gz http://compbio.cs.princeton.edu/conservation/conservation_code.tar.gz; \ ); \ mv $$t/*.tar.?z ./ .PHONY: override_dh_auto_build -override_dh_auto_build: man +override_dh_auto_build: man scripts %: dh $@ --parallel --with python2 @@ -42,10 +32,28 @@ .PHONY: man man: $(MANS) +.PHONY: scripts +scripts: $(SCRIPTS) + +$(SCRIPTS) : % : %.py + cp -f $< $@ + +ChangeLog: score_conservation.py + # Courtesy of Jakub Wilk: + sed -n -e '/# [0-9/]\{8\}/ { s/# // p }' < $< > $@ + +.PHONY: override_dh_installchangelogs +override_dh_installchangelogs: ChangeLog + dh_installchangelogs + %.1: %.1.pod sed -e 's|__docdir__|$(docdir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__VERSION__|$(VERSION)|g;' "$<" | \ pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell echo "$(basename $@)" | tr '[:lower:]' '[:upper:]') > "$@" +.PHONY: override_dh_install +override_dh_install: + dh_install -X._ + .PHONY: override_dh_auto_clean override_dh_auto_clean: - rm -f $(MANS) + rm -f $(MANS) $(SCRIPTS) ChangeLog _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
