diff tools/ngs_simulation/grinder_multiple_outputs.py @ 1:7d26d64539b2

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ngs_simulation/grinder_multiple_outputs.py	Mon Sep 19 01:07:28 2011 -0400
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+
+"""
+Move files create by Grinder to a location where it is going to be recognized by
+Galaxy as multiple output files with the right format. See
+http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple Output Files
+Example: python grinder_move_outputs output_dir output_id
+Author: Florent Angly
+"""
+
+import sys, os, re
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def __main__():
+    # Get output dir and ID
+    args = sys.argv
+    output_dir = args[1]
+    output_id  = args[2]
+
+    # Move Grinder files to the proper output
+    # Grinder filenames look like this
+    #   grinder-ranks.txt
+    #   grinder-reads.fa
+    #   grinder-reads.qual
+    #   grinder-1-ranks.txt
+    #   grinder-1-reads.fa
+    #   grinder-1-reads.qual
+    #   grinder-2-ranks.txt
+    #   grinder-2-reads.fa
+    #   grinder-2-reads.qual
+
+    p = re.compile(output_id)
+    q = re.compile('-(\d+)-')
+    r = re.compile('-(\w+)$')
+    
+
+    for fname in os.listdir(output_dir):
+
+        # Skip files that do not start with the output_id
+        source = os.path.join( output_dir, fname )
+        basename, extension = os.path.splitext(fname)
+        if not p.match(fname):
+           continue
+
+        # Assign the dataset format
+        if extension == '.txt': 
+           format = 'text'
+        elif extension == '.fa':
+           format = 'fasta'
+        elif extension == '.fna':
+           format = 'fasta'
+        elif extension == '.faa':
+           format = 'fasta'
+        elif extension == '.fasta':
+           format = 'fasta'
+        elif extension == '.fq':
+           format = 'fastq'
+        elif extension == '.fastq':
+           format = 'fastq'
+        elif extension == '.qual':
+           format = 'qual'
+        else:
+           stop_err( 'Error: File %s had the unknown extension %s' % ( fname, extension ) )
+        
+        # Assign the dataset name
+        name = ''
+        match = q.search(basename)
+        if match != None:
+          lib_num = match.group(1)
+          name = 'lib%s' % lib_num
+
+        match = r.search(basename)
+        if match == None:
+          stop_err( 'Error: File with basename %s did not have a recognized name' % (basename) )
+        
+        lib_type = match.group(1)
+        if format == 'qual':
+          lib_type = 'qual'
+
+        name = name + '-' + lib_type        
+
+        # Move the dataset to the proper place
+        optional_spec = 'asdf'
+        destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s_%s' % ( output_id, name, format, optional_spec ) )
+
+        print "moving %s to %s" % (source, destination)
+
+        try:
+          os.rename(source, destination)
+        except Exception, e:
+          stop_err( 'Error: ' + str( e ) )
+
+if __name__ == "__main__": __main__()