--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cuffmerge_wrapper.py	Tue Oct 01 12:57:24 2013 -0400
@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+
+# Supports Cuffmerge versions 1.3 and newer.
+
+import optparse, os, shutil, subprocess, sys, tempfile
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+# Copied from sam_to_bam.py:
+def check_seq_file( dbkey, cached_seqs_pointer_file ):
+    seq_path = ''
+    for line in open( cached_seqs_pointer_file ):
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ) and line.startswith( 'index' ):
+            fields = line.split( '\t' )
+            if len( fields ) < 3:
+                continue
+            if fields[1] == dbkey:
+                seq_path = fields[2].strip()
+                break
+    return seq_path
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-g', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.' )
+    parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffmerge to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.')
+    parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' )
+    
+    
+    # Wrapper / Galaxy options.
+    parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
+    parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
+    parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
+    
+    # Outputs.
+    parser.add_option( '', '--merged-transcripts', dest='merged_transcripts' )
+    
+    (options, args) = parser.parse_args()
+    
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='cuffmerge -v 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'merge_cuff_asms v' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Cuffmerge version\n' )
+        
+    # Set/link to sequence file.
+    if options.use_seq_data:
+        if options.ref_file != 'None':
+            # Sequence data from history.
+            # Create symbolic link to ref_file so that index will be created in working directory.
+            seq_path = "ref.fa"
+            os.symlink( options.ref_file, seq_path  )
+        else:
+            # Sequence data from loc file.
+            cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' )
+            if not os.path.exists( cached_seqs_pointer_file ):
+                stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file )
+            # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa,
+            # and the equCab2.fa file will contain fasta sequences.
+            seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
+            if seq_path == '':
+                stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey  )
+    
+    # Build command.
+    
+    # Base.
+    cmd = "cuffmerge -o cm_output "
+    
+    # Add options.
+    if options.num_threads:
+        cmd += ( " -p %i " % int ( options.num_threads ) )
+    if options.ref_annotation:
+        cmd += " -g %s " % options.ref_annotation
+    if options.use_seq_data:
+        cmd += " -s %s " % seq_path
+        
+    # Add input files to a file.
+    inputs_file_name = tempfile.NamedTemporaryFile( dir="." ).name
+    inputs_file = open( inputs_file_name, 'w' )
+    for arg in args:
+        inputs_file.write( arg + "\n" )
+    inputs_file.close()
+    cmd += inputs_file_name
+
+    # Debugging.
+    print cmd
+    
+    # Run command.
+    try:        
+        tmp_name = tempfile.NamedTemporaryFile( dir="." ).name
+        tmp_stderr = open( tmp_name, 'wb' )
+        proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        
+        # Get stderr, allowing for case where it's very large.
+        tmp_stderr = open( tmp_name, 'rb' )
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stderr.close()
+        
+        # Error checking.
+        if returncode != 0:
+            raise Exception, stderr
+            
+        if len( open( "cm_output/merged.gtf", 'rb' ).read().strip() ) == 0:
+            raise Exception, 'The output file is empty, there may be an error with your input file or settings.'
+            
+        # Copy outputs.
+        shutil.copyfile( "cm_output/merged.gtf" , options.merged_transcripts )    
+            
+    except Exception, e:
+        stop_err( 'Error running cuffmerge. ' + str( e ) )
+        
+if __name__=="__main__": __main__()