--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dwgsim_wrapper.py	Sun Aug 14 20:07:45 2011 -0400
@@ -0,0 +1,168 @@
+#!/usr/bin/env python
+
+"""
+Runs DWGSIM
+
+usage: dwgsim_wrapper.py [options]
+    -e,--errorOne=e: base/color error rate of the first read [0.020]
+    -E,--errorTwo=E: base/color error rate of the second read [0.020]
+    -d,--innertDist=d: inner distance between the two ends [500]
+    -s,--stdev=s: standard deviation [50]
+    -N,--numReads=N: number of read pairs [1000000]
+    -1,--lengthOne=1: length of the first read [70]
+    -2,--lengthTwo=2: length of the second read [70]
+    -r,--mutRate=r: rate of mutations [0.0010]
+    -R,--fracIndels=R: fraction of indels [0.10]
+    -X,--indelExt=X: probability an indel is extended [0.30]
+    -y,--randProb=y: probability of a random DNA read [0.10]
+    -n,--maxN=n: maximum number of Ns allowed in a given read [0]
+    -c,--colorSpace=c: generate reads in color space (SOLiD reads)
+    -S,--strand=S: strand 0: default, 1: same strand, 2: opposite strand
+    -H,--haploid=H: haploid mode
+    -f,--fasta=f: the reference genome FASTA
+    -3,--outputBFAST=3: the BFAST output FASTQ
+    -4,--outputBWA1=4: the first BWA output FASTQ
+    -5,--outputBWA2=5: the second BWA output FASTQ
+    -6,--outputMutations=6: the output mutations TXT
+"""
+
+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( '-e', '--errorOne', dest='errorOne', type='float', help='base/color error rate of the first read' )
+    parser.add_option( '-E', '--errorTwo', dest='errorTwo', type='float', help='base/color error rate of the second read' )
+    parser.add_option( '-d', '--innertDist', dest='innertDist', type='int', help='inner distance between the two ends' )
+    parser.add_option( '-s', '--stdev', dest='stdev', type='float', help='standard deviation' )
+    parser.add_option( '-N', '--numReads', dest='numReads', type='int', help='number of read pairs' )
+    parser.add_option( '-1', '--lengthOne', dest='lengthOne', type='int', help='length of the first read' )
+    parser.add_option( '-2', '--lengthTwo', dest='lengthTwo', type='int', help='length of the second read' )
+    parser.add_option( '-r', '--mutRate', dest='mutRate', type='float', help='rate of mutations' )
+    parser.add_option( '-R', '--fracIndels', dest='fracIndels', type='float', help='fraction of indels' )
+    parser.add_option( '-X', '--indelExt', dest='indelExt', type='float', help='probability an indel is extended' )
+    parser.add_option( '-y', '--randProb', dest='randProb', type='float', help='probability of a random DNA read' )
+    parser.add_option( '-n', '--maxN', dest='maxN', type='int', help='maximum number of Ns allowed in a given read' )
+    parser.add_option( '-c', '--colorSpace', action='store_true', dest='colorSpace', default=False, help='generate reads in color space (SOLiD reads)' )
+    parser.add_option( '-S', '--strand', dest='strand', type='choice', default='0', choices=('0', '1', '2'), help='strand 0: default, 1: same strand, 2: opposite strand' )
+    parser.add_option( '-H', '--haploid', action='store_true', dest='haploid', default=False, help='haploid mode' )
+    parser.add_option( '-f', '--fasta', dest='fasta', help='The reference genome fasta' )
+    parser.add_option( '-3', '--outputBFAST', dest='outputBFAST', help='the BFAST output FASTQ' )
+    parser.add_option( '-4', '--outputBWA1', dest='outputBWA1', help='the first BWA output FASTQ' )
+    parser.add_option( '-5', '--outputBWA2', dest='outputBWA2', help='the second BWA output FASTQ' )
+    parser.add_option( '-6', '--outputMutations', dest='outputMutations', help='the output mutations TXT' )
+    
+    (options, args) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='dwgsim 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 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:
+        reference_filepath = tempfile.NamedTemporaryFile( dir=tmp_dir, suffix='.fa' ).name
+        os.symlink( options.fasta, reference_filepath )
+        assert reference_filepath and os.path.exists( reference_filepath ), 'A valid genome reference was not provided.'
+        tmp_dir = '%s/' % tempfile.mkdtemp()
+        dwgsim_output_prefix = "dwgsim_output_prefix"
+        dwgsim_cmd = 'dwgsim -e %s -E %s -d %s -s %s -N %s -1 %s -2 %s -r %s -R %s -X %s -y %s -n %s' % \
+                (options.errorOne, \
+                options.errorTwo, \
+                options.innertDist, \
+                options.stdev, \
+                options.numReads, \
+                options.lengthOne, \
+                options.lengthTwo, \
+                options.mutRate, \
+                options.fracIndels, \
+                options.indelExt, \
+                options.randProb, \
+                options.maxN)
+        if options.colorSpace:
+            dwgsim_cmd = dwgsim_cmd + ' -c'
+        if options.haploid:
+            dwgsim_cmd = dwgsim_cmd + ' -H'
+        dwgsim_cmd = dwgsim_cmd + ' ' + options.fasta
+        dwgsim_cmd = dwgsim_cmd + ' ' + tmp_dir + '/' + dwgsim_output_prefix
+
+        # need to nest try-except in try-finally to handle 2.4
+        try:
+            # dwgsim
+            run_process ( dwgsim_cmd, 'dwgsim', tmp_dir, buffsize )
+            # Move files
+            cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.mutations.txt' + ' ' + options.outputMutations
+            run_process ( cmd, 'mv #1', tmp_dir, buffsize )
+            cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.bfast.fastq' + ' ' + options.outputBFAST
+            run_process ( cmd, 'mv #2', tmp_dir, buffsize )
+            cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.bwa.read1.fastq' + ' ' + options.outputBWA1
+            run_process ( cmd, 'mv #3', tmp_dir, buffsize )
+            cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.bwa.read2.fastq' + ' ' + options.outputBWA2
+            run_process ( cmd, 'mv #4', tmp_dir, buffsize )
+            # check that there are results in the output file
+            check_output ( options.outputMutations, True )
+            check_output ( options.outputBFAST, False )
+            check_output ( options.outputBWA1, False )
+            check_output ( options.outputBWA2, False )
+            sys.stdout.write( 'DWGSIM successful' )
+        except Exception, e:
+            stop_err( 'DWGSIM failed.\n' + str( e ) )
+    finally:
+        # clean up temp dir
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+
+if __name__=="__main__": __main__()