# HG changeset patch # User drosofff # Date 1399846705 14400 # Node ID eed2a141eb0c8aeea37ad3e0f955367113526483 # Parent 05ae11c21834193a34ea41da8cb146c0afaf62da Uploaded diff -r 05ae11c21834 -r eed2a141eb0c sRbowtie_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sRbowtie_wrapper.py Sun May 11 18:18:25 2014 -0400 @@ -0,0 +1,106 @@ +#!/usr/bin/env python +# generic bowtie wrapper for bowtie, small RNA oriented +# version 1 17-1-2014 +# Usage sRbowtie_wrapper.py <1 input_fasta_file> <2 alignment method> <3 -v mismatches> <4 out_type> <5 buildIndexIfHistory> <6 fasta/bowtie index> <7 bowtie output> <8 ali_fasta> <9 unali_fasta> + +import sys, re, os, subprocess, shlex, tempfile, shutil + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def bowtieCommandLiner (alignment_method, v_mis, out_type, aligned, unaligned, input, index, output): + if alignment_method=="RNA": + x = "-v %s -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8" % v_mis + elif alignment_method=="unique": + x = "-v %s -m 1 -p 12 --suppress 6,7,8" % v_mis + elif alignment_method=="multiple": + x = "-v %s -M 1 --best --strata -p 12 --suppress 6,7,8" % v_mis + elif alignment_method=="k_option": + x = "-v %s -k 1 --best -p 12 --suppress 6,7,8" % v_mis + elif alignment_method=="n_option": + x = "-n %s -M 1 --best -p 12 --suppress 6,7,8" % v_mis + elif alignment_method=="a_option": + x = "-v %s -a --best -p 12 --suppress 6,7,8" % v_mis + if aligned == "None" and unaligned == "None": fasta_command = "" + elif aligned != "None" and unaligned == "None": fasta_command= " --al %s" % aligned + elif aligned == "None" and unaligned != "None": fasta_command = " --un %s" % unaligned + else: fasta_command = " --al %s --un %s" % (aligned, unaligned) + x = x + fasta_command + if out_type == "tabular": + return "bowtie %s %s -f %s > %s" % (x, index, input, output) + elif out_type=="sam": + return "bowtie %s -S %s -f %s > %s" % (x, index, input, output) + elif out_type=="bam": + return "bowtie %s -S %s -f %s |samtools view -bS - > %s" % (x, index, input, output) + +def bowtie_squash(fasta): + # make temp directory for placement of indices and copy reference file there if necessary + tmp_index_dir = tempfile.mkdtemp() + ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) + ref_file_name = ref_file.name + ref_file.close() # by default, this action delete the temporary file ! + os.symlink( fasta, ref_file_name ) # now there is a symlink between the fasta source file and the deleted ref_file name + cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name ) # this will work with the bowtie command line but we have to change the working dir ! + try: + FNULL = open(os.devnull, 'w') + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name # a full path temp file to tmp_index_dir is created. just a string + tmp_stderr = open( tmp, 'wb' ) # creates and open the file handler + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL ) # fileno() method return the file descriptor number of tmp_stderr / stderr=tmp_stderr.fileno() + # here I played a while a finish by redirecting everythin in dev/null. Clean later tmp_stderr calls + returncode = proc.wait() + tmp_stderr.close() + FNULL.close() + sys.stdout.write(cmd1 + "\n") + except Exception, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Error indexing reference sequence\n' + str( e ) ) + # no Cleaning if no Exception, to be cleaned later after bowtie alignment + index_full_path = os.path.join(tmp_index_dir, ref_file_name) # bowtie fashion path (without extention) ... + return tmp_index_dir, index_full_path + +def bowtie_alignment(command_line, flyPreIndexed=''): + # make temp directory just for stderr + tmp_index_dir = tempfile.mkdtemp() + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + # conditional statement for sorted bam generation viewable in Trackster + if "samtools" in command_line: + target_file = command_line.split()[-1] # recover the final output file name + path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam") + path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted") + first_command_line = " ".join(command_line.split()[:-3]) + " -o " + path_to_unsortedBam + " - " # example: bowtie -v 0 -M 1 --best --strata -p 12 --suppress 6,7,8 -S /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam - + second_command_line = "samtools sort %s %s" % (path_to_unsortedBam, path_to_sortedBam) # Be carreful : this indeed will generate an unsorted.bam.sorted.bam file, NOT a unsorted.bam.sorted file + p = subprocess.Popen(args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) + returncode = p.wait() + sys.stdout.write("%s\n" % first_command_line + str(returncode)) + p = subprocess.Popen(args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) + returncode = p.wait() + sys.stdout.write("\n%s\n" % second_command_line + str(returncode)) + if os.path.isfile(path_to_sortedBam + ".bam"): + shutil.copy2(path_to_sortedBam + ".bam", target_file) + else: + p = subprocess.Popen(args=command_line, shell=True, stderr=tmp_stderr.fileno()) + returncode = p.wait() + sys.stdout.write(command_line + "\n") + tmp_stderr.close() + ## cleaning if the index was created in the fly + if os.path.exists( flyPreIndexed ): + shutil.rmtree( flyPreIndexed ) + # cleaning tmp files and directories + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + return + +def __main__(): + F = open (sys.argv[-3], "w") + if sys.argv[5] == "history": + tmp_dir, index_path = bowtie_squash(sys.argv[6]) + else: + tmp_dir, index_path = "dummy/dymmy", sys.argv[6] + command_line = bowtieCommandLiner(sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[-2], sys.argv[-1], sys.argv[1], index_path, sys.argv[7]) + bowtie_alignment(command_line, flyPreIndexed=tmp_dir) + F.close() +if __name__=="__main__": __main__()