Mercurial > repos > drosofff > bowtie_for_smallrna
view sRbowtie/sRbowtie.py @ 4:303baef87cb7 draft
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author | drosofff |
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date | Sat, 21 Jun 2014 09:54:35 -0400 |
parents | 324c3142ca0f |
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#!/usr/bin/env python # small RNA oriented bowtie wrapper # version 1.01 29-5-2014 # Usage sRbowtie.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> <10 --num-threads \${GALAXY_SLOTS:-4}> # current rev: for bowtie __norc, move from --supress 2,6,7,8 to --supress 6,7,8. Future Parser must be updated to take into account this standardisation # To Do: # implement an arg parser # Christophe Antoniewski <drosofff@gmail.com> import sys, os, subprocess, 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, pslots="12"): if alignment_method=="RNA": x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % (v_mis, pslots) elif alignment_method=="unique": x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots) elif alignment_method=="multiple": x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % (v_mis, pslots) elif alignment_method=="k_option": x = "-v %s -k 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots) elif alignment_method=="n_option": x = "-n %s -M 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots) elif alignment_method=="a_option": x = "-v %s -a --best -p %s --suppress 6,7,8" % (v_mis, pslots) 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): tmp_index_dir = tempfile.mkdtemp() # make temp directory for bowtie indexes ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close() # by default, delete the temporary file, but ref_file.name is now stored in ref_file_name os.symlink( fasta, ref_file_name ) # symlink between the fasta source file and the deleted ref_file name cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name ) # bowtie command line, which will work after changing dir (cwd=tmp_index_dir) try: FNULL = open(os.devnull, 'w') tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name # a path string for a temp file in tmp_index_dir. Just a string tmp_stderr = open( tmp, 'wb' ) # creates and open a file handler pointing to the temp file proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL ) # both stderr and stdout of bowtie-build are redirected in dev/null 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, tmp_index_dir has to be cleaned 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) # generates an "unsorted.bam.sorted.bam file", NOT an "unsorted.bam.sorted" file p = subprocess.Popen(args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) # fileno() method return the file descriptor number of tmp_stderr 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[7], "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[8], sys.argv[9], sys.argv[1], index_path, sys.argv[7], sys.argv[10]) bowtie_alignment(command_line, flyPreIndexed=tmp_dir) F.close() if __name__=="__main__": __main__()