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1 #!/usr/bin/env python
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2 import argparse
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3 import subprocess
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4 import os
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5 import shlex
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6
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7 def createIndex(fname):
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8 """
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9 Create an index for a file, return where it is
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10 """
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11 d = os.mkdir("index_dir")
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12 os.link(fname, "index_dir/genome.fa")
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13 cmd = "{}/bwameth.py index index_dir/genome.fa".format(os.path.dirname(__file__))
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14 proc = subprocess.Popen(args=shlex.split(cmd))
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15 returncode = proc.wait()
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16 if returncode != 0:
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17 raise Exception("Error during '%s'" % cmd)
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18 return "index_dir/genome.fa"
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19
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20
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21 parser = argparse.ArgumentParser(description="A wrapper around bwameth for Galaxy. There's minimal argument checking done")
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22 parser.add_argument('-p', '--numThreads', type=int, default=4, help="number of threads")
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23 parser.add_argument('--makeIndex', help="Given a fasta file, index it")
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24 parser.add_argument('--premadeIndex', help="If an index already exists, this is the fasta file associated with it (the index files must be in the same directory")
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25 parser.add_argument('--readGroup', help="The read group text, if desired")
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26 parser.add_argument('files', nargs="+", help="Fasta files (possibly gzipped, if the file names end in .gz)")
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27 args = parser.parse_args()
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28
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29 if "makeIndex" in args:
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30 ifile = createIndex(args.makeIndex)
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31 else:
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32 ifile = args.premadeIndex
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33
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34 files = " ".join(['{}'.format(x) for x in args.files])
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35 if "readGroup" in args:
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36 files = "{} --read-group '{}'".format(files, args.readGroup)
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37
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38 cmd = "{}/bwameth.py -p {} '{}' {} | samtools view -Su - - | samtools sort -@ {} -o output.bam -".format(os.path.dirname(__file__), args.numThreads, ifile, files, args.numThreads)
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39 proc = subprocess.Popen(args=shlex.split(cmd))
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40 returncode = proc.wait()
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41 if returncode != 0:
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42 raise Exception("Error during '%s'" % cmd)
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