[med-svn] r12392 - in trunk/packages/conservation-code/trunk/debian: . patches

[Laszlo Kajan]

Author: lkajan-guest
Date: 2012-10-11 20:50:46 +0000 (Thu, 11 Oct 2012)
New Revision: 12392

Added:
   trunk/packages/conservation-code/trunk/debian/patches/stockholm_format
Modified:
   trunk/packages/conservation-code/trunk/debian/changelog
   trunk/packages/conservation-code/trunk/debian/patches/series
   trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod
Log:
allow parsing of Stockholm format as well

Modified: trunk/packages/conservation-code/trunk/debian/changelog
===================================================================
--- trunk/packages/conservation-code/trunk/debian/changelog	2012-10-11 19:59:08 UTC (rev 12391)
+++ trunk/packages/conservation-code/trunk/debian/changelog	2012-10-11 20:50:46 UTC (rev 12392)
@@ -1,3 +1,9 @@
+conservation-code (20110309.0-2) UNRELEASED; urgency=low
+
+  * Allow parsing of Stockholm format as well.
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Thu, 11 Oct 2012 22:50:04 +0200
+
 conservation-code (20110309.0-1) unstable; urgency=low
 
   * Initial release. (Closes: #690058)

Modified: trunk/packages/conservation-code/trunk/debian/patches/series
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/series	2012-10-11 19:59:08 UTC (rev 12391)
+++ trunk/packages/conservation-code/trunk/debian/patches/series	2012-10-11 20:50:46 UTC (rev 12392)
@@ -3,3 +3,4 @@
 numpy.numarray
 default_matrix_path
 optimize_loop
+stockholm_format

Added: trunk/packages/conservation-code/trunk/debian/patches/stockholm_format
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/stockholm_format	                        (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/patches/stockholm_format	2012-10-11 20:50:46 UTC (rev 12392)
@@ -0,0 +1,53 @@
+Author: Laszlo Kajan <lkajan at rostlab.org>
+Description: allow parsing of Stockholm format as well
+Forwarded: no
+--- a/score_conservation.py
++++ b/score_conservation.py
+@@ -84,6 +84,7 @@
+ ################################################################################
+ 
+ import math, sys, getopt
++import re
+ # numarray imported below
+ 
+ PSEUDOCOUNT = .0000001
+@@ -679,12 +680,14 @@
+     return names, alignment
+ 	
+ def read_clustal_alignment(filename):
+-    """ Read in the alignment stored in the CLUSTAL file, filename. Return
++    """ Read in the alignment stored in the CLUSTAL or Stockholm file, filename. Return
+     two lists: the names and sequences. """
+ 
+     names = []
+     alignment = []
+ 
++    re_stock_markup = re.compile('^#=')
++
+     f = open(filename)
+ 
+     for line in f:
+@@ -692,16 +695,20 @@
+ 	if len(line) == 0: continue
+ 	if '*' in line: continue
+ 
+-	if 'CLUSTAL' in line: continue
++	if line[0:7] == 'CLUSTAL': continue
++	if line[0:11] == '# STOCKHOLM': continue
++	if line[0:2] == '//': continue
++
++	if re_stock_markup.match(line): continue
+ 
+ 	t = line.split()
+ 
+ 	if len(t) == 2 and t[1][0] in iupac_alphabet:
+ 	    if t[0] not in names:
+ 		names.append(t[0])
+-		alignment.append(t[1].upper().replace('B', 'D').replace('Z', 'Q').replace('X', '-').replace('\r', ''))
++		alignment.append(t[1].upper().replace('B', 'D').replace('Z', 'Q').replace('X', '-').replace('\r', '').replace('.', '-'))
+ 	    else:
+-		alignment[names.index(t[0])] += t[1].upper().replace('B', 'D').replace('Z', 'Q').replace('X','-').replace('\r', '')
++		alignment[names.index(t[0])] += t[1].upper().replace('B', 'D').replace('Z', 'Q').replace('X','-').replace('\r', '').replace('.', '-')
+ 		   
+     return names, alignment
+ 

Modified: trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod
===================================================================
--- trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod	2012-10-11 19:59:08 UTC (rev 12391)
+++ trunk/packages/conservation-code/trunk/debian/score_conservation.1.pod	2012-10-11 20:50:46 UTC (rev 12392)
@@ -10,7 +10,7 @@
 
 =head1 DESCRIPTION
 
-Score protein sequence conservation in B<ALIGNFILE>.  B<ALIGNFILE> must be in FASTA or CLUSTAL format.
+Score protein sequence conservation in B<ALIGNFILE>.  B<ALIGNFILE> must be in FASTA, CLUSTAL or Stockholm format.
 
 The following conservation scoring methods are implemented:
  * sum of pairs
@@ -32,7 +32,7 @@
 Jensen-Shannon divergence and a window B<-w> of I<3>.
 
 The sequence-specific output can be used as the conservation input for
-concavity.
+concavity(1).
 
 Conservation is highly predictive in identifying catalytic sites and
 residues near bound ligands.