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1 import argparse
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2 import sys
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3 import re
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4
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5 if __name__ == '__main__':
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6
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7 desc = "Convert Strelka Makefile into a sub-Makefile used STRICTLY for parallelization by chromosome in Galaxy"
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8 parser = argparse.ArgumentParser(description=desc)
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9 parser.add_argument(
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10 "-m", "--makefile",
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11 required=True,
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12 help="Input Must be a Strelka Makefile"
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13 )
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14 parser.add_argument(
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15 "-c", "--chrom",
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16 type=str,
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17 required=False,
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18 help="Chromosome present in the Strelka Makefile"
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19 )
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20 parser.add_argument(
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21 "-cf", "--chrom_file",
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22 required=False,
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23 help="Chromosome File separated by newline"
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24 )
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25 parser.add_argument(
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26 '-o', '--output',
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27 required=True,
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28 help="Output Makefile"
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29 )
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30 args = parser.parse_args()
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31
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32 if (not args.chrom and not args.chrom_file) or (args.chrom and args.chrom_file):
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33 sys.exit('Must define a single chromosome entry or a single chromosome file')
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34
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35 chromosomes = [];
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36
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37 if args.chrom_file:
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38 chromosomes = open(args.chrom_file).read().splitlines()
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39
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40 if args.chrom:
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41 chromosomes = [args.chrom]
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42 add_at_end = []
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43 makefile_in = open(args.makefile, 'r')
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44 makefile_out = open(args.output, 'w')
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45
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46 for line in makefile_in:
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47 if line.startswith('script_dir'):
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48 makefile_out.write(line)
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49 elif line.startswith('call_script'):
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50 makefile_out.write(line)
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51 elif line.startswith('filter_script'):
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52 makefile_out.write(line)
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53 elif line.startswith('finish_script'):
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54 makefile_out.write(line)
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55 elif line.startswith('script_dir'):
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56 makefile_out.write(line)
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57 elif line.startswith('config_file'):
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58 makefile_out.write(line)
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59 elif line.startswith('analysis_dir'):
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60 makefile_out.write(line)
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61 elif line.startswith('results_dir'):
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62 makefile_out.write(line)
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63 elif line.startswith('get_chrom_dir'):
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64 makefile_out.write(line)
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65 elif line.startswith('get_chrom_task'):
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66 makefile_out.write(line)
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67 elif line.startswith('get_bin_task'):
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68 makefile_out.write(line)
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69 makefile_out.write('\n')
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70 elif line.startswith('all:'):
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71 makefile_out.write('all:\n')
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72 elif re.search("--chrom=", line):
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73 if re.search(''.join(["\s|".join(chromosomes),'\s']), line):
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74 if re.search('bin', line):
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75 makefile_out.write(line)
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76 else:
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77 add_at_end.append(line)
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78
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79 makefile_in.close()
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80 for line in add_at_end:
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81 makefile_out.write(line)
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82 makefile_out.close()
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