--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dwgsim_eval_wrapper.py	Sun Aug 14 20:08:43 2011 -0400
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+
+"""
+Runs DWGSIM_EVAL
+
+usage: dwgsim_eval_wrapper.py [options]
+    -a,--alignmentScore=a: split alignments by alignment score instead of mapping quality
+    -b,--bwa=b: alignments are from BWA
+    -c,--colorSpace=c: color space alignments
+    -d,--scoreFactor=d: divide quality/alignment score by this factor
+    -g,--wiggle=g: gap "wiggle"
+    -n,--numReads=n: number of raw input paired-end reads (otherwise, inferred from all SAM records present).
+    -q,--minMapq=q: consider only alignments with this mapping quality or greater.
+    -z,--singleEnd=z: input contains only single end reads
+    -S,--sam=s: input SAM file
+    -B,--bam=B: input BAM file
+    -p,--printIncorrect=p: print incorrect alignments
+    -s,--numSnps=s: consider only alignments with the number of specified SNPs
+    -e,--numErrors=e: consider only alignments with the number of specified errors
+    -i,--indels=i: consider only alignments with indels
+    -o,--output=u: The file to save the output 
+"""
+
+import optparse, os, shutil, subprocess, sys, tempfile
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def run_process ( cmd, name, tmp_dir, buffsize ):
+    try:
+        tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+        tmp_stderr = open( tmp, 'wb' )
+        proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        # get stderr, allowing for case where it's very large
+        tmp_stderr = open( tmp, 'rb' )
+        stderr = ''
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stderr.close()
+        if returncode != 0:
+            raise Exception, stderr
+    except Exception, e:
+        raise Exception, 'Error in \'' + name + '\'. \n' + str( e )
+
+def check_output ( output, canBeEmpty ):
+    if 0 < os.path.getsize( output ):
+        return True
+    elif False == canBeEmpty:
+        raise Exception, 'The output file is empty:' + output
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+
+    parser.add_option( '-a', '--alignmentScore', action='store_true', dest='alignmentScore', default=False, help='split alignments by alignment score instead of mapping quality' )
+    parser.add_option( '-b', '--bwa', action='store_true', dest='bwa', default=False, help='alignments are from BWA' )
+    parser.add_option( '-c', '--colorSpace', action='store_true', dest='colorSpace', default=False, help='generate reads in color space (SOLiD reads)' )
+    parser.add_option( '-d', '--scoreFactor', dest='scoreFactor', type='int', help='divide quality/alignment score by this factor' )
+    parser.add_option( '-g', '--wiggle', dest='wiggle', type='int', help='gap "wiggle"' )
+    parser.add_option( '-n', '--numReads', dest='numReads', type='int', help='number of raw input paired-end reads (otherwise, inferred from all SAM records present).' )
+    parser.add_option( '-q', '--minMapq', dest='minMapq', type='int', help='consider only alignments with this mapping quality or greater.' )
+    parser.add_option( '-z', '--singleEnd', action='store_true', dest='singleEnd', default=False, help='input contains only single end reads' )
+    parser.add_option( '-S', '--sam', dest='sam', default=None, help='input SAM' )
+    parser.add_option( '-B', '--bam', dest='bam', default=None, help='input BAM' )
+    parser.add_option( '-p', '--printIncorrect', action='store_true', dest='printIncorrect', default=False, help='print incorrect alignments' )
+    parser.add_option( '-s', '--numSnps', dest='numSnps', type="int", help='consider only alignments with the number of specified SNPs' )
+    parser.add_option( '-e', '--numErrors', dest='numErrors', type="int", default=False, help='consider only alignments with the number of specified errors' )
+    parser.add_option( '-i', '--indels', action='store_true', dest='indels', default=False, help='consider only alignments with indels' )
+    parser.add_option( '-o', '--output', dest='output', help='The file to save the output' )
+    
+    (options, args) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='dwgsim_eval 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( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine DWGSIM_EVAL version\n' )
+
+    buffsize = 1048576
+
+    # make temp directory for dwgsim, requires trailing slash
+    tmp_dir = '%s/' % tempfile.mkdtemp()
+
+    #'generic' options used in all dwgsim commands here
+
+    try:
+        tmp_dir = '%s/' % tempfile.mkdtemp()
+        dwgsim_eval_cmd = 'dwgsim_eval'
+        if True == options.alignmentScore:
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' -a'
+        if True == options.bwa:
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' -b'
+        if True == options.colorSpace:
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' -c'
+        use_p = False
+        if 0 <= options.numSnps:
+            use_p = True
+            dwgsim_eval_cmd = dwgsim_eval_cmd + (' -s %s' % options.numSnps)
+        if 0 <= options.numErrors:
+            use_p = True
+            dwgsim_eval_cmd = dwgsim_eval_cmd + (' -e %s' % options.numErrors)
+        if True == options.indels:
+            use_p = True
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' -i'
+        if True == use_p or True == options.printIncorrect:
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' -p'
+        if True == options.singleEnd:
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' -z'
+        dwgsim_eval_cmd = '%s -d %s -g %s -n %s -q %s' % (dwgsim_eval_cmd, \
+                options.scoreFactor, \
+                options.wiggle, \
+                options.numReads, \
+                options.minMapq)
+        if None != options.sam:
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' -S ' + options.sam
+        elif None != options.bam:
+            dwgsim_eval_cmd = dwgsim_eval_cmd + ' ' + options.bam
+        else:
+            raise Exception, 'Input file was neither a SAM nor BAM'
+        dwgsim_eval_cmd = dwgsim_eval_cmd + ' > ' + options.output
+
+        # need to nest try-except in try-finally to handle 2.4
+        try:
+            # dwgsim
+            run_process ( dwgsim_eval_cmd, 'dwgsim', tmp_dir, buffsize )
+            # check that there are results in the output file
+            check_output ( options.output, False )
+            sys.stdout.write( 'DWGSIM_EVAL successful' )
+        except Exception, e:
+            stop_err( 'DWGSIM_EVAL failed.\n' + str( e ) )
+    finally:
+        # clean up temp dir
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+
+if __name__=="__main__": __main__()