From 047c1bff2f9950d273bcac61c7b2eccefe2fd0fc Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 8 Mar 2012 11:09:14 -0500
Subject: [PATCH] Enable fasta_to_len conversion to use only first word in
 title; this is standards compliant and used by default for automatic
 conversion.

---
 lib/galaxy/datatypes/converters/fasta_to_len.py | 10 +++++++---
 tools/fasta_tools/fasta_compute_length.py       |  2 +-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.py b/lib/galaxy/datatypes/converters/fasta_to_len.py
index 26f0856bd4e..d604d8dd101 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.py
@@ -9,7 +9,7 @@ import sys, os
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
-def compute_fasta_length( fasta_file, out_file, keep_first_char ):
+def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word=False ):
     
     infile = fasta_file
     out = open( out_file, 'w')
@@ -32,6 +32,8 @@ def compute_fasta_length( fasta_file, out_file, keep_first_char ):
             continue
         if line[0] == '>':
             if first_entry == False:
+                if keep_first_word:
+                    fasta_title = fasta_title.split()[0]
                 out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
             else:
                 first_entry = False
@@ -41,8 +43,10 @@ def compute_fasta_length( fasta_file, out_file, keep_first_char ):
             seq_len += len(line)
 
     # last fasta-entry
+    if keep_first_word:
+        fasta_title = fasta_title.split()[0]
     out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
     out.close()
 
-if __name__ == "__main__" : 
-    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3] )
\ No newline at end of file
+if __name__ == "__main__" :
+    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True )
\ No newline at end of file
diff --git a/tools/fasta_tools/fasta_compute_length.py b/tools/fasta_tools/fasta_compute_length.py
index 57a257bb7df..5080bd3ca26 100644
--- a/tools/fasta_tools/fasta_compute_length.py
+++ b/tools/fasta_tools/fasta_compute_length.py
@@ -6,4 +6,4 @@ Uses fasta_to_len converter code.
 import sys
 from galaxy.datatypes.converters.fasta_to_len import compute_fasta_length
 
-compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3])
\ No newline at end of file
+compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], False )
\ No newline at end of file