Mercurial > repos > drosofff > msp_sr_bowtie
annotate sRbowtie.py @ 29:04685a1b3de1 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
| author | drosofff |
|---|---|
| date | Sun, 02 Jul 2017 12:34:18 -0400 |
| parents | a0bde9b84ca6 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 # small RNA oriented bowtie wrapper | |
| 3 # version 1.5 17-7-2014: arg parser implementation | |
| 4 # 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}> | |
| 5 # 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 | |
| 6 # Christophe Antoniewski <drosofff@gmail.com> | |
| 7 | |
| 1 | 8 import sys |
| 9 import os | |
| 10 import subprocess | |
| 11 import tempfile | |
| 12 import shutil | |
| 13 import argparse | |
| 14 | |
| 0 | 15 |
| 16 def Parser(): | |
| 1 | 17 the_parser = argparse.ArgumentParser( |
| 18 description="bowtie wrapper for small fasta reads") | |
| 19 the_parser.add_argument( | |
| 20 '--input', action="store", type=str, help="input file") | |
| 21 the_parser.add_argument( | |
| 22 '--input-format', dest="input_format", action="store", type=str, help="fasta or fastq") | |
| 23 the_parser.add_argument('--method', action="store", type=str, | |
| 24 help="RNA, unique, multiple, k_option, n_option, a_option") | |
| 25 the_parser.add_argument('--v-mismatches', dest="v_mismatches", action="store", | |
| 26 type=str, help="number of mismatches allowed for the alignments") | |
| 27 the_parser.add_argument( | |
| 28 '--output-format', dest="output_format", action="store", type=str, help="tabular, sam, bam") | |
| 29 the_parser.add_argument( | |
| 30 '--output', action="store", type=str, help="output file path") | |
| 31 the_parser.add_argument( | |
| 32 '--index-from', dest="index_from", action="store", type=str, help="indexed or history") | |
| 33 the_parser.add_argument('--index-source', dest="index_source", | |
| 34 action="store", type=str, help="file path to the index source") | |
| 35 the_parser.add_argument( | |
| 36 '--aligned', action="store", type=str, help="aligned read file path, maybe None") | |
| 37 the_parser.add_argument('--unaligned', action="store", | |
| 38 type=str, help="unaligned read file path, maybe None") | |
| 39 the_parser.add_argument('--num-threads', dest="num_threads", | |
| 40 action="store", type=str, help="number of bowtie threads") | |
| 41 args = the_parser.parse_args() | |
| 42 return args | |
| 0 | 43 |
| 1 | 44 |
| 45 def stop_err(msg): | |
| 46 sys.stderr.write('%s\n' % msg) | |
| 0 | 47 sys.exit() |
| 48 | |
| 1 | 49 |
| 50 def bowtieCommandLiner(alignment_method="RNA", v_mis="1", out_type="tabular", | |
| 51 aligned="None", unaligned="None", input_format="fasta", input="path", | |
| 52 index="path", output="path", pslots="4"): | |
| 53 if input_format == "fasta": | |
| 54 input_format = "-f" | |
|
2
316124e85b8d
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents:
1
diff
changeset
|
55 elif (input_format == "fastq") or (input_format == "fastqsanger"): |
| 1 | 56 input_format = "-q" |
| 57 else: | |
| 58 raise Exception('input format must be one of fasta or fastq') | |
| 59 if alignment_method == "RNA": | |
| 60 x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % ( | |
| 61 v_mis, pslots) | |
| 62 elif alignment_method == "unique": | |
| 63 x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots) | |
| 64 elif alignment_method == "multiple": | |
| 65 x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % ( | |
| 66 v_mis, pslots) | |
| 67 elif alignment_method == "k_option": | |
| 0 | 68 x = "-v %s -k 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots) |
| 1 | 69 elif alignment_method == "n_option": |
| 0 | 70 x = "-n %s -M 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots) |
| 1 | 71 elif alignment_method == "a_option": |
| 0 | 72 x = "-v %s -a --best -p %s --suppress 6,7,8" % (v_mis, pslots) |
| 1 | 73 if aligned == "None" and unaligned == "None": |
| 74 fasta_command = "" | |
| 75 elif aligned != "None" and unaligned == "None": | |
| 76 fasta_command = " --al %s" % aligned | |
| 77 elif aligned == "None" and unaligned != "None": | |
| 78 fasta_command = " --un %s" % unaligned | |
| 79 else: | |
| 80 fasta_command = " --al %s --un %s" % (aligned, unaligned) | |
| 0 | 81 x = x + fasta_command |
| 82 if out_type == "tabular": | |
| 1 | 83 return "bowtie %s %s %s %s > %s" % (x, index, input_format, input, output) |
| 84 elif out_type == "sam": | |
| 85 return "bowtie %s -S %s %s %s > %s" % (x, index, input_format, input, output) | |
| 86 elif out_type == "bam": | |
| 87 return "bowtie %s -S %s %s %s |samtools view -bS - > %s" % ( | |
| 88 x, index, input_format, input, output) | |
| 89 | |
| 0 | 90 |
| 91 def bowtie_squash(fasta): | |
| 1 | 92 # make temp directory for bowtie indexes |
| 93 tmp_index_dir = tempfile.mkdtemp() | |
| 94 ref_file = tempfile.NamedTemporaryFile(dir=tmp_index_dir) | |
| 95 ref_file_name = ref_file.name | |
| 96 # by default, delete the temporary file, but ref_file.name is now stored | |
| 97 # in ref_file_name | |
| 98 ref_file.close() | |
| 99 # symlink between the fasta source file and the deleted ref_file name | |
| 100 os.symlink(fasta, ref_file_name) | |
| 101 # bowtie command line, which will work after changing dir | |
| 102 # (cwd=tmp_index_dir) | |
| 103 cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name) | |
| 104 try: | |
| 105 FNULL = open(os.devnull, 'w') | |
| 106 # a path string for a temp file in tmp_index_dir. Just a string | |
| 107 tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name | |
| 108 # creates and open a file handler pointing to the temp file | |
| 109 tmp_stderr = open(tmp, 'wb') | |
| 110 # both stderr and stdout of bowtie-build are redirected in dev/null | |
| 111 proc = subprocess.Popen( | |
| 112 args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL) | |
| 113 returncode = proc.wait() | |
| 114 tmp_stderr.close() | |
| 115 FNULL.close() | |
| 116 sys.stdout.write(cmd1 + "\n") | |
| 117 except Exception as e: | |
| 118 # clean up temp dir | |
| 119 if os.path.exists(tmp_index_dir): | |
| 120 shutil.rmtree(tmp_index_dir) | |
| 121 stop_err('Error indexing reference sequence\n' + str(e)) | |
| 122 # no Cleaning if no Exception, tmp_index_dir has to be cleaned after | |
| 123 # bowtie_alignment() | |
| 124 # bowtie fashion path without extention | |
| 125 index_full_path = os.path.join(tmp_index_dir, ref_file_name) | |
| 126 return tmp_index_dir, index_full_path | |
| 127 | |
| 128 | |
| 0 | 129 def bowtie_alignment(command_line, flyPreIndexed=''): |
| 1 | 130 # make temp directory just for stderr |
| 131 tmp_index_dir = tempfile.mkdtemp() | |
| 132 tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name | |
| 133 tmp_stderr = open(tmp, 'wb') | |
| 134 # conditional statement for sorted bam generation viewable in Trackster | |
| 135 if "samtools" in command_line: | |
| 136 # recover the final output file name | |
| 137 target_file = command_line.split()[-1] | |
| 138 path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam") | |
| 139 path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted") | |
| 140 first_command_line = " ".join( | |
| 141 command_line.split()[:-3]) + " -o " + path_to_unsortedBam + " - " | |
| 142 # example: bowtie -v 0 -M 1 --best --strata -p 12 --suppress 6,7,8 -S | |
| 143 # /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f | |
| 144 # /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat | |
| 145 # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam - | |
| 146 # generates an "unsorted.bam.sorted.bam file", NOT an | |
| 147 # "unsorted.bam.sorted" file | |
|
7
5d82f9b15957
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
5
diff
changeset
|
148 second_command_line = "samtools sort %s %s" % ( |
| 1 | 149 path_to_unsortedBam, path_to_sortedBam) |
| 150 # fileno() method return the file descriptor number of tmp_stderr | |
| 151 p = subprocess.Popen( | |
| 152 args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) | |
| 153 returncode = p.wait() | |
| 154 sys.stdout.write("%s\n" % first_command_line + str(returncode)) | |
| 155 p = subprocess.Popen( | |
| 156 args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) | |
| 157 returncode = p.wait() | |
| 158 sys.stdout.write("\n%s\n" % second_command_line + str(returncode)) | |
| 159 if os.path.isfile(path_to_sortedBam + ".bam"): | |
| 160 shutil.copy2(path_to_sortedBam + ".bam", target_file) | |
| 161 else: | |
| 162 p = subprocess.Popen( | |
| 163 args=command_line, shell=True, stderr=tmp_stderr.fileno()) | |
| 164 returncode = p.wait() | |
| 165 sys.stdout.write(command_line + "\n") | |
| 166 tmp_stderr.close() | |
| 167 # cleaning if the index was created in the fly | |
| 168 if os.path.exists(flyPreIndexed): | |
| 169 shutil.rmtree(flyPreIndexed) | |
| 170 # cleaning tmp files and directories | |
| 171 if os.path.exists(tmp_index_dir): | |
| 172 shutil.rmtree(tmp_index_dir) | |
| 173 return | |
| 174 | |
| 0 | 175 |
| 176 def __main__(): | |
| 1 | 177 args = Parser() |
| 178 F = open(args.output, "w") | |
| 179 if args.index_from == "history": | |
| 180 tmp_dir, index_path = bowtie_squash(args.index_source) | |
| 181 else: | |
| 182 tmp_dir, index_path = "dummy/dymmy", args.index_source | |
| 183 command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format, | |
|
12
a0bde9b84ca6
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07
drosofff
parents:
7
diff
changeset
|
184 args.aligned, args.unaligned, args.input_format, args.input, |
| 1 | 185 index_path, args.output, args.num_threads) |
| 186 bowtie_alignment(command_line, flyPreIndexed=tmp_dir) | |
| 187 F.close() | |
| 188 if __name__ == "__main__": | |
| 189 __main__() |