[med-svn] r12385 - in trunk/packages/conservation-code/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Oct 11 11:32:25 UTC 2012
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 <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lkajan at rostlab.org>
-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 <lkajan at rostlab.org>
+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 <lkajan at rostlab.org>
+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 <lkajan at rostlab.org>
+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 <lkajan at rostlab.org>
-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 <lkajan at rostlab.org>
+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
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