--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/smalt_wrapper.py	Wed Feb 13 13:27:44 2013 -0500
@@ -0,0 +1,195 @@
+#!/usr/bin/env python
+
+"""
+Runs Smalt on single-end or paired-end data.
+Produces a SAM file containing the mappings.
+Works with Smalt version 0.7.1.
+
+usage: smalt_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 __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to use' )
+    parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
+    parser.add_option( '-f', '--input1', dest='fastq', help='The (forward) fastq file to use for the mapping' )
+    parser.add_option( '-F', '--input2', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data' )
+    parser.add_option( '-u', '--output', dest='output', help='The file to save the output (SAM format)' )
+    parser.add_option( '-g', '--genAlignType', dest='genAlignType', help='The type of pairing (single or paired)' )
+    parser.add_option( '-p', '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
+    parser.add_option( '-s', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' )
+    parser.add_option( '-x', '--exhaustiveSearch', dest='exhaustiveSearch', help='This flag triggers a more exhaustive search for alignments at the cost of decreased speed' )
+    parser.add_option( '-c', '--minCover', dest='minCover', help='Only consider mappings where the k-mer word seeds cover the query read to a minimum extent' )
+    parser.add_option( '-d', '--scorDiff', dest='scorDiff', help='Set a threshold of the Smith-Waterman alignment score relative to the maximum score' )
+    parser.add_option( '-i', '--insertMax', dest='insertMax', help='Maximum insert size (Only in paired-end mode)' )
+    parser.add_option( '-j', '--insertMin', dest='insertMin', help='Minimum insert size (Only in paired-end mode)' )
+    parser.add_option( '-l', '--pairTyp', dest='pairTyp', help='Type of read pair library, can be either pe, mp or pp' )
+    parser.add_option( '-m', '--minScor', dest='minScor', help='Sets an absolute threshold of the Smith-Waterman scores' )
+    parser.add_option( '-a', '--partialAlignments', dest='partialAlignments', help='Report partial alignments if they are complementary on the read (split reads)' )
+    parser.add_option( '-q', '--minBasq', dest='minBasq', help='Sets a base quality threshold (0 <= minbasq <= 10, default 0)' )
+    parser.add_option( '-e', '--seed', dest='seed', help='If <seed> >= 0 report an alignment selected at random where there are multiple mappings with the same best alignment score. With <seed> = 0 (default) a seed is derived from the current calendar time. If <seed> < 0 reads with multiple best mappings are reported as "not mapped".' )
+    parser.add_option( '-w', '--complexityWeighted', dest='complexityWeighted', help='Smith-Waterman scores are complexity weighted' )
+    parser.add_option( '-y', '--minId', dest='minId', help='Sets an identity threshold for a mapping to be reported' )
+    parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
+    parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
+    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+    (options, args) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='smalt 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( 'SMALT %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine SMALT version\n' )
+
+    fastq = options.fastq
+    if options.rfastq:
+         rfastq = options.rfastq
+
+    # make temp directory for placement of indices
+    tmp_index_dir = tempfile.mkdtemp()
+    tmp_dir = tempfile.mkdtemp()
+    # index if necessary
+    if options.fileSource == 'history' and not options.do_not_build_index:
+        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
+        ref_file_name = ref_file.name
+        ref_file.close()
+        os.symlink( options.ref, ref_file_name )
+        cmd1 = 'smalt index %s %s' % ( ref_file_name, ref_file_name )
+        try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_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 = ''
+            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()
+            if returncode != 0:
+                raise Exception, stderr
+        except Exception, e:
+            # clean up temp dirs
+            if os.path.exists( tmp_index_dir ):
+                shutil.rmtree( tmp_index_dir )
+            if os.path.exists( tmp_dir ):
+                shutil.rmtree( tmp_dir )
+            stop_err( 'Error indexing reference sequence. ' + str( e ) )
+    else:
+        ref_file_name = options.ref
+
+    # set up aligning and generate aligning command options
+    if options.params == 'pre_set':
+        aligning_cmds = '-n %s ' % ( options.threads )
+        gen_alignment_cmds = ''
+    else:
+        if options.exhaustiveSearch == 'true':
+            exhaustiveSearch = '-x'
+            minCover = '-c %s' % options.minCover
+        else:
+            exhaustiveSearch = ''
+            minCover = ''
+        if options.partialAlignments == 'true':
+            partialAlignments = '-x'
+        else:
+            partialAlignments = ''
+        if options.complexityWeighted == 'true':
+            complexityWeighted = '-w'
+        else:
+            complexityWeighted = ''
+        aligning_cmds = '-d %s -m %s -q %s -r %s -y %s' % \
+                        ( options.scorDiff, options.minScor, options.minBasq, options.seed, options.minId )
+        if options.genAlignType == 'paired':
+            gen_alignment_cmds = '-i %s -j %s -l %s' % ( options.insertMax, options.insertMin, options.pairTyp )
+        else:
+            gen_alignment_cmds = ''
+    # prepare actual aligning and generate aligning commands
+    if options.genAlignType == 'paired':
+        cmd = 'smalt map %s %s -o %s %s %s ' % ( aligning_cmds, gen_alignment_cmds, options.output, ref_file_name, fastq, rfastq )
+    else:
+        cmd = 'smalt map %s -o %s %s %s ' % ( aligning_cmds, options.output, ref_file_name, fastq )
+    # perform alignments
+    buffsize = 1048576
+    try:
+        # need to nest try-except in try-finally to handle 2.4
+        try:
+            # align
+            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 aligning sequence. ' + str( e )
+            # remove header if necessary
+            if options.suppressHeader == 'true':
+                tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
+                tmp_out_name = tmp_out.name
+                tmp_out.close()
+                try:
+                    shutil.move( options.output, tmp_out_name )
+                except Exception, e:
+                    raise Exception, 'Error moving output file before removing headers. ' + str( e )
+                fout = file( options.output, 'w' )
+                for line in file( tmp_out.name, 'r' ):
+                    if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
+                        fout.write( line )
+                fout.close()
+            # check that there are results in the output file
+            if os.path.getsize( options.output ) > 0:
+                sys.stdout.write( 'SMALT run on %s-end data' % options.genAlignType )
+            else:
+                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 alignment failed.\n' + str( e ) )
+    finally:
+        # clean up temp dir
+        if os.path.exists( tmp_index_dir ):
+            shutil.rmtree( tmp_index_dir )
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+
+if __name__=="__main__": __main__()