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annotate misc/sscs_diff.py @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents af383638de66
children
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1 #!/usr/bin/env python
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2 from __future__ import division
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3 import sys
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4 import argparse
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5 import subprocess
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6
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7 OPT_DEFAULTS = {}
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8 USAGE = "%(prog)s [options]"
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9 DESCRIPTION = """Find differences between the SSCS produced by one version of the pipeline and
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10 another, when working on the same input MSA's."""
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11 EPILOG = """Warning: This injects raw command-line arguments into shell commands and executes them.
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12 """
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13
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14
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15 def main(argv):
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16
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17 parser = argparse.ArgumentParser(description=DESCRIPTION, epilog=EPILOG)
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18 parser.set_defaults(**OPT_DEFAULTS)
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19
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20 parser.add_argument('sscs_before', metavar='sscs.all.before.fa',
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21 help='SSCSs from earlier version (can be gzipped).')
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22 parser.add_argument('sscs_after', metavar='sscs.all.after.fa',
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23 help='SSCSs from later version (can be gzipped).')
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24 parser.add_argument('-b', '--before', metavar='sscs.all.before.diffs.fa', required=True,
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25 help='Output SSCSs from earlier version that differ from the SSCS in the later version here.')
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26 parser.add_argument('-a', '--after', metavar='sscs.all.after.diffs.fa', required=True,
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27 help='Output SSCSs from later version that differ from the SSCS in the earlier version here.')
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28
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29 args = parser.parse_args(argv[1:])
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30
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31 sscs_before = {}
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32 if args.sscs_before.endswith('.gz'):
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33 command = 'gunzip -c {} | paste - - | sort'.format(args.sscs_before)
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34 else:
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35 command = 'cat {} | paste - - | sort'.format(args.sscs_before)
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36 process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
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37 for line in process.stdout:
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38 fields = line.rstrip('\r\n').split('\t')
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39 name = fields[0].lstrip('>').split()[0]
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40 seq = fields[1]
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41 sscs_before[name] = seq
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42
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43 before_fh = open(args.before, 'w')
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44 after_fh = open(args.after, 'w')
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45 diffs = {}
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46 if args.sscs_after.endswith('.gz'):
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47 command = 'gunzip -c {} | paste - - | sort'.format(args.sscs_after)
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48 else:
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49 command = 'cat {} | paste - - | sort'.format(args.sscs_after)
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50 process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
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51 for line in process.stdout:
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52 fields = line.rstrip('\r\n').split('\t')
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53 header = fields[0].lstrip('>')
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54 name, fam_size = header.split()
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55 seq_after = fields[1]
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56 if name in sscs_before:
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57 seq_before = sscs_before[name]
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58 if seq_before != seq_after:
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59 diffs[name] = (seq_before, seq_after)
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60 before_fh.write('>{} {}\n'.format(name, fam_size))
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61 before_fh.write(seq_before+'\n')
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62 after_fh.write('>{} {}\n'.format(name, fam_size))
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63 after_fh.write(seq_after+'\n')
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64 before_fh.close()
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65 after_fh.close()
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66
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67
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68 def fail(message):
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69 sys.stderr.write(message+"\n")
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70 sys.exit(1)
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71
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72
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73 if __name__ == '__main__':
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74 sys.exit(main(sys.argv))