--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa_mem.py	Tue Mar 18 07:49:22 2014 -0400
@@ -0,0 +1,273 @@
+# -*- coding: utf-8 -*-
+#!/usr/bin/env python
+## yufei.luo@gustave.roussy 22/07/2013
+## Copyright © 2014 CRS4 Srl. http://www.crs4.it/
+## Modified by:
+## Nicola Soranzo <nicola.soranzo@crs4.it>
+
+"""
+Runs BWA on single-end or paired-end data.
+Produces a SAM file containing the mappings.
+Works with BWA version >= 0.7.5.
+NOTICE: In this wrapper, we only use 'mem' for mapping step.
+
+usage: bwa_mem.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 check_is_double_encoded( fastq ):
+    # check that first read is bases, not one base followed by numbers
+    bases = [ 'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N' ]
+    nums = [ '0', '1', '2', '3' ]
+    for line in file( fastq, 'rb'):
+        if not line.strip() or line.startswith( '@' ):
+            continue
+        if len( [ b for b in line.strip() if b in nums ] ) > 0:
+            return False
+        elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ):
+            return True
+        else:
+            raise Exception, 'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space'
+    raise Exception, 'There is no non-comment and non-blank line in your FASTQ file'
+
+def __main__():
+    descr = "bwa_mem.py: Map (long length) reads against a reference genome with BWA-MEM."
+    parser = optparse.OptionParser(description=descr)
+    parser.add_option( '-t', '--threads', default=1, help='The number of threads to use [1]' )
+    parser.add_option( '--ref', help='The reference genome to use or index' )
+    parser.add_option( '-f', '--fastq', help='The (forward) fastq file to use for the mapping' )
+    parser.add_option( '-F', '--rfastq', help='The reverse fastq file to use for mapping if paired-end data' )
+    parser.add_option( '-u', '--output', help='The file to save the output (SAM format)' )
+    parser.add_option( '-g', '--genAlignType', help='The type of pairing (single or paired)' )
+    parser.add_option( '--params', help='Parameter setting to use (pre_set or full)' )
+    parser.add_option( '-s', '--fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' )
+    parser.add_option( '-D', '--dbkey', help='Dbkey for reference genome' )
+
+    parser.add_option( '-k', '--minEditDistSeed', default=19, type=int, help='Minimum edit distance to the seed [19]' )
+    parser.add_option( '-w', '--bandWidth', default=100, type=int, help='Band width for banded alignment [100]' )
+    parser.add_option( '-d', '--offDiagonal', default=100, type=int, help='off-diagonal X-dropoff [100]' )
+    parser.add_option( '-r', '--internalSeeds', default=1.5, type=float, help='look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]' )
+    parser.add_option( '-c', '--seedsOccurrence', default=10000, type=int, help='skip seeds with more than INT occurrences [10000]' )
+    parser.add_option( '-S', '--mateRescue', default=False, help='skip mate rescue' )
+    parser.add_option( '-P', '--skipPairing', default=False, help='skpe pairing, mate rescue performed unless -S also in use' )
+    parser.add_option( '-A', '--seqMatch', default=1, type=int, help='score of a sequence match' )
+    parser.add_option( '-B', '--mismatch', default=4, type=int, help='penalty for a mismatch' )
+    parser.add_option( '-O', '--gapOpen', default=6, type=int, help='gap open penalty' )
+    parser.add_option( '-E', '--gapExtension', default=None, help='gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]' )
+    parser.add_option( '-L', '--clipping', default=5, type=int, help='penalty for clipping [5]' )
+    parser.add_option( '-U', '--unpairedReadpair', default=17, type=int, help='penalty for an unpaired read pair [17]' )
+    parser.add_option( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' )
+    parser.add_option( '--rgid', help='Read group identifier' )
+    parser.add_option( '--rgsm', help='Sample' )
+    parser.add_option( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT', 'PACBIO' ], help='Platform/technology used to produce the reads' )
+    parser.add_option( '--rglb', help='Library name' )
+    parser.add_option( '--rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' )
+    parser.add_option( '--rgcn', help='Sequencing center that produced the read' )
+    parser.add_option( '--rgds', help='Description' )
+    parser.add_option( '--rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' )
+    parser.add_option( '--rgfo', help='Flow order' )
+    parser.add_option( '--rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' )
+    parser.add_option( '--rgpg', help='Programs used for processing the read group' )
+    parser.add_option( '--rgpi', help='Predicted median insert size' )
+    parser.add_option( '-T', '--minScore', default=30, type=int, help='minimum score to output [30]' )
+    parser.add_option( '-M', '--mark', default=False, help='mark shorter split hits as secondary (for Picard/GATK compatibility)' )
+    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error('Wrong number of arguments')
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='bwa 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( 'BWA %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine BWA 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':
+        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
+        ref_file_name = ref_file.name
+        ref_file.close()
+        os.symlink( options.ref, ref_file_name )
+        # determine which indexing algorithm to use, based on size
+        try:
+            size = os.stat( options.ref ).st_size
+            if size <= 2**30:
+                indexingAlg = 'is'
+            else:
+                indexingAlg = 'bwtsw'
+        except:
+            indexingAlg = 'is'
+        indexing_cmds = '-a %s' % indexingAlg
+        cmd1 = 'bwa index %s %s' % ( indexing_cmds, 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
+    # if options.illumina13qual:
+    #     illumina_quals = "-I"
+    # else:
+    #     illumina_quals = ""
+
+    # set up aligning and generate aligning command args
+    start_cmds = '-t %s ' % options.threads
+    if options.params == 'pre_set':
+        # aligning_cmds = '-t %s %s' % ( options.threads, illumina_quals )
+        #start_cmds = '-t %s ' % options.threads
+        end_cmds = ' '
+        print start_cmds, end_cmds
+
+    else:
+        end_cmds = '-k %s -w %s -d %s -r %s -c %s -A %s -B %s -O %s -L %s -U %s -T %s ' % (options.minEditDistSeed, options.bandWidth, options.offDiagonal, options.internalSeeds, options.seedsOccurrence, options.seqMatch, options.mismatch, options.gapOpen, options.clipping, options.unpairedReadpair, options.minScore)
+        if options.mateRescue:
+            end_cmds += '-S '
+            if options.skipPairing:
+                end_cmds += '-P '
+        else:
+            if options.skipPairing:
+                print "Option Error and will not be considered, you should also choose 'skip mate rescue -S' option! "
+        if options.gapExtension != None:
+            end_cmds += '-E %s ' % options.gapExtension
+
+        if options.rgid:
+            if not options.rglb or not options.rgpl or not options.rgsm or not options.rglb:
+                stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
+            # readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
+            readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
+            if options.rgpu:
+                readGroup += '\tPU:%s' % options.rgpu
+            if options.rgcn:
+                readGroup += '\tCN:%s' % options.rgcn
+            if options.rgds:
+                readGroup += '\tDS:%s' % options.rgds
+            if options.rgdt:
+                readGroup += '\tDT:%s' % options.rgdt
+            if options.rgfo:
+                readGroup += '\tFO:%s' % options.rgfo
+            if options.rgks:
+                readGroup += '\tKS:%s' % options.rgks
+            if options.rgpg:
+                readGroup += '\tPG:%s' % options.rgpg
+            if options.rgpi:
+                readGroup += '\tPI:%s' % options.rgpi
+            end_cmds += ' -R "%s" ' % readGroup
+
+        if options.interPairEnd:
+            end_cmds += '-p %s ' % options.interPairEnd
+        if options.mark:
+            end_cmds += '-M '
+
+
+    if options.genAlignType == 'paired':
+        cmd = 'bwa mem %s %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, rfastq, end_cmds, options.output )
+    else:
+        cmd = 'bwa mem %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, end_cmds, options.output )
+
+  # perform alignments
+    buffsize = 1048576
+    try:
+        # 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' )
+                print "The cmd is %s" % cmd
+                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 generating alignments. ' + 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( 'BWA 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__()