--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/srma_wrapper.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,195 @@
+#!/usr/bin/env python
+
+"""
+Runs SRMA on a SAM/BAM file;
+TODO: more documentation
+
+usage: srma_wrapper.py [options]
+
+See below for options
+"""
+
+import optparse, os, shutil, subprocess, sys, tempfile
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def parseRefLoc( refLoc, refUID ):
+    for line in open( refLoc ):
+        if not line.startswith( '#' ):
+            fields = line.strip().split( '\t' )
+            if len( fields ) >= 3:
+                if fields[0] == refUID:
+                    return fields[1]
+    return None
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to index and use' )
+    parser.add_option( '-u', '--refUID', dest='refUID', help='The pre-index reference genome unique Identifier' )
+    parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' )
+    parser.add_option( '-i', '--input', dest='input', help='The SAM/BAM input file' )
+    parser.add_option( '-I', '--inputIndex', dest='inputIndex', help='The SAM/BAM input index file' )
+    parser.add_option( '-o', '--output', dest='output', help='The SAM/BAM output file' )
+    parser.add_option( '-O', '--offset', dest='offset', help='The alignment offset' )
+    parser.add_option( '-Q', '--minMappingQuality', dest='minMappingQuality', help='The minimum mapping quality' )
+    parser.add_option( '-P', '--minAlleleProbability', dest='minAlleleProbability', help='The minimum allele probability conditioned on coverage (for the binomial quantile).' )
+    parser.add_option( '-C', '--minAlleleCoverage', dest='minAlleleCoverage', help='The minimum haploid coverage for the consensus' )
+    parser.add_option( '-R', '--range', dest='range', help='A range to examine' )
+    parser.add_option( '-c', '--correctBases', dest='correctBases', help='Correct bases ' )
+    parser.add_option( '-q', '--useSequenceQualities', dest='useSequenceQualities', help='Use sequence qualities ' )
+    parser.add_option( '-M', '--maxHeapSize', dest='maxHeapSize', help='The maximum number of nodes on the heap before re-alignment is ignored' )
+    parser.add_option( '-s', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one from history (indexed or history)' )
+    parser.add_option( '-p', '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
+    parser.add_option( '-j', '--jarBin', dest='jarBin', default='', help='The path to where jars are stored' )
+    parser.add_option( '-f', '--jarFile', dest='jarFile', help='The file name of the jar file to use')
+    (options, args) = parser.parse_args()
+
+    # make temp directory for srma
+    tmp_dir = tempfile.mkdtemp()
+    buffsize = 1048576
+
+    # set up reference filenames
+    reference_filepath_name = None
+    # need to create SRMA dict and Samtools fai files for custom genome
+    if options.fileSource == 'history':
+        try:
+            reference_filepath = tempfile.NamedTemporaryFile( dir=tmp_dir, suffix='.fa' )
+            reference_filepath_name = reference_filepath.name
+            reference_filepath.close()
+            fai_filepath_name = '%s.fai' % reference_filepath_name
+            dict_filepath_name = reference_filepath_name.replace( '.fa', '.dict' )
+            os.symlink( options.ref, reference_filepath_name )
+            # create fai file using Samtools
+            index_fai_cmd = 'samtools faidx %s' % reference_filepath_name
+            try:
+                tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+                tmp_stderr = open( tmp, 'wb' )
+                proc = subprocess.Popen( args=index_fai_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:
+                # clean up temp dir
+                if os.path.exists( tmp_dir ):
+                    shutil.rmtree( tmp_dir )
+                stop_err( 'Error creating Samtools index for custom genome file: %s\n' % str( e ) )
+            # create dict file using SRMA
+            dict_cmd = 'java -cp "%s" net.sf.picard.sam.CreateSequenceDictionary R=%s O=%s' % ( os.path.join( options.jarBin, options.jarFile ), reference_filepath_name, dict_filepath_name )
+            try:
+                tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+                tmp_stderr = open( tmp, 'wb' )
+                proc = subprocess.Popen( args=dict_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:
+                # clean up temp dir
+                if os.path.exists( tmp_dir ):
+                    shutil.rmtree( tmp_dir )
+                stop_err( 'Error creating index for custom genome file: %s\n' % str( e ) )
+        except Exception, e:
+            # clean up temp dir
+            if os.path.exists( tmp_dir ):
+                shutil.rmtree( tmp_dir )
+            stop_err( 'Problem handling SRMA index (dict file) for custom genome file: %s\n' % str( e ) )
+    # using built-in dict/index files
+    else:
+        if options.ref:
+            reference_filepath_name = options.ref
+        else:
+            reference_filepath_name = parseRefLoc( options.refLocation, options.refUID )
+    if reference_filepath_name is None:
+        raise ValueError( 'A valid genome reference was not provided.' )
+
+    # set up aligning and generate aligning command options
+    if options.params == 'pre_set':
+        srma_cmds = ''
+    else:
+        if options.useSequenceQualities == 'true':
+            useSequenceQualities = 'true'
+        else:
+            useSequenceQualities = 'false'
+        ranges = 'null'
+        if options.range == 'None':
+            range = 'null'
+        else:
+            range = options.range
+        srma_cmds = "OFFSET=%s MIN_MAPQ=%s MINIMUM_ALLELE_PROBABILITY=%s MINIMUM_ALLELE_COVERAGE=%s RANGES=%s RANGE=%s CORRECT_BASES=%s USE_SEQUENCE_QUALITIES=%s MAX_HEAP_SIZE=%s" % ( options.offset, options.minMappingQuality, options.minAlleleProbability, options.minAlleleCoverage, ranges, range, options.correctBases, options.useSequenceQualities, options.maxHeapSize )
+
+    # perform alignments
+    buffsize = 1048576
+    try:
+        #symlink input bam and index files due to the naming conventions required by srma here
+        input_bam_filename = os.path.join( tmp_dir, '%s.bam' % os.path.split( options.input )[-1] )
+        os.symlink( options.input, input_bam_filename )
+        input_bai_filename = "%s.bai" % os.path.splitext( input_bam_filename )[0]
+        os.symlink( options.inputIndex, input_bai_filename )
+
+        #create a temp output name, ending in .bam due to required naming conventions? unkown if required
+        output_bam_filename = os.path.join( tmp_dir, "%s.bam" % os.path.split( options.output )[-1] )
+        # generate commandline
+        cmd = 'java -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds )
+
+        # need to nest try-except in try-finally to handle 2.4
+        try:
+            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 executing SRMA. ' + str( e )
+            # move file from temp location (with .bam name) to provided path
+            shutil.move( output_bam_filename, options.output )
+            # check that there are results in the output file
+            if os.path.getsize( options.output ) <= 0:
+                raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
+        except Exception, e:
+            stop_err( 'The re-alignment failed.\n' + str( e ) )
+    finally:
+        # clean up temp dir
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+
+if __name__=="__main__": __main__()