# HG changeset patch
# User boris
# Date 1374270570 14400
# Node ID 8d0a0c488a8e4ed4ab5a7ba0d3b830f67cfd8fc1
# Parent  dc78c20610a14a1909743a4555f0ac94261859e0
the "_major" suffix is now suppressed. Only the minor allele sequences are labeled "_minor"

diff -r dc78c20610a1 -r 8d0a0c488a8e getalleleseq.py
--- a/getalleleseq.py	Tue Jun 25 00:47:05 2013 -0400
+++ b/getalleleseq.py	Fri Jul 19 17:49:30 2013 -0400
@@ -25,7 +25,7 @@
 #                        this directory
 #
 # The expected columns in the alleles table follow Nicholas Stoler's
-# Count alleles tool format.  See Count alleles in Galaxy's tool shed
+# Variant Annotator tool format.  See Variant Annotator in Galaxy's tool shed
 # http://testtoolshed.g2.bx.psu.edu/repos/nick/allele_counts_1 for more details
 #
 # Expected columns:
@@ -68,7 +68,8 @@
 
 def printseq(sample,allele,seq,output):
     """Print out sequence"""
-    print >> output, '>{0}_{1}'.format(sample,allele)
+    #print >> output, '>{0}_{1}'.format(sample,allele)
+    print >> output, '>{0}{1}'.format(sample,allele)
     for i in range(0,len(seq),70):
         print >> output, ''.join(seq[i:i+70])
 
@@ -95,7 +96,8 @@
     # Single file for all major allele sequences in FASTA multiple alignment
     for sample in samples:
         sequence = createseq(sample,'major',args.seq_length,table)
-        printseq(sample,'major',sequence,major_out)
+        #printseq(sample,'major',sequence,major_out)
+        printseq(sample,'',sequence,major_out)
     major_out.close()
 
     # Sample specific minor allele sequence in FASTA format
@@ -112,7 +114,8 @@
             minor_name = sample+'-minor.fa'
         minor_out = open(os.path.join(args.minor_dir, minor_name), 'w+')
         sequence = createseq(sample,'minor',args.seq_length,table)
-        printseq(sample,'minor',sequence,minor_out)
+        #printseq(sample,'minor',sequence,minor_out)
+        printseq(sample,'_minor',sequence,minor_out)
         minor_out.close()
 
 if __name__ == "__main__": main()
\ No newline at end of file