[hg] galaxy 1474: Reverting extract_genomic_dna and blat_wrapper...

classic Classic list List threaded Threaded
1 message Options
| Threaded
Open this post in threaded view
|

[hg] galaxy 1474: Reverting extract_genomic_dna and blat_wrapper...

greg
details:   http://www.bx.psu.edu/hg/galaxy/rev/cea8c4d68ad0
changeset: 1474:cea8c4d68ad0
user:      Greg Von Kuster <[hidden email]>
date:      Thu Aug 21 08:54:51 2008 -0400
description:
Reverting extract_genomic_dna and blat_wrapper tools to rev 1472.

2 file(s) affected in this change:

tools/extract/extract_genomic_dna.py
tools/metag_tools/blat_wrapper.py

diffs (42 lines):

diff -r 8cda62b46162 -r cea8c4d68ad0 tools/extract/extract_genomic_dna.py
--- a/tools/extract/extract_genomic_dna.py Tue Aug 19 13:35:44 2008 -0400
+++ b/tools/extract/extract_genomic_dna.py Thu Aug 21 08:54:51 2008 -0400
@@ -35,7 +35,7 @@
     for line in open( nib_file ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ) and line.startswith( 'seq' ):
-            fields = line.split()
+            fields = line.split( '\t' )
             if len( fields ) < 3:
                 continue
             if fields[1] == dbkey:
@@ -49,7 +49,7 @@
     for line in open( twobit_file ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ):
-            fields = line.split()
+            fields = line.split( '\t' )
             if len( fields ) < 2:
                 continue
             if fields[0] == dbkey:
diff -r 8cda62b46162 -r cea8c4d68ad0 tools/metag_tools/blat_wrapper.py
--- a/tools/metag_tools/blat_wrapper.py Tue Aug 19 13:35:44 2008 -0400
+++ b/tools/metag_tools/blat_wrapper.py Thu Aug 21 08:54:51 2008 -0400
@@ -15,7 +15,7 @@
     for i, line in enumerate( file( nib_file ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ):
-            fields = line.split()
+            fields = line.split( '\t' )
             if len( fields ) < 3:
                 continue
             if fields[0] == 'seq':
@@ -31,7 +31,7 @@
     for i, line in enumerate( file( twobit_file ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ):
-            fields = line.split()
+            fields = line.split( '\t' )
             if len( fields ) < 2:
                 continue
             twobits[( fields[0] )] = fields[1]