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1 #!/usr/bin/env python
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2 """
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3 Parse the FR-HIT output file format.
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4 """
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5
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6 from __future__ import division
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7 import sys, getopt
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8
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9 class FRHITFragment:
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10 """
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11 Represents a fragment match to a reference genome.
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12 """
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13
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14 def __init__(self, frhit_string):
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15 fields = frhit_string.rstrip().split()
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16
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17 self.name = fields[0]
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18 self.refseq = fields[8].split('|')[3]
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19 self.location = int(fields[9])
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20 self.identity = float(fields[7][:-1])
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21 self.length = int(fields[3])
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22
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23 def __repr__(self):
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24 out = []
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25 out.append("Name: %s\n" % self.name)
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26 out.append("Location: %d\n" % self.location)
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27 out.append("Identity: %4.1f\n" % self.identity)
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28 return ''.join(out)
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29
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30
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31 def FRHITFile(filename):
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32 """
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33 Parses the fr-hit format file, returning FRHITFragment objects.
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34
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35 This is a generator, so that there is no need to store a full list of
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36 fragments in memory if it's not necessary to do so.
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37 """
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38
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39 f = open(filename, 'rb')
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40
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41 for line in f:
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42 yield FRHITFragment(line)
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43
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44 f.close()
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45
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46
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47 if __name__ == '__main__':
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48 opts, args = getopt.getopt(sys.argv[1:], 'h')
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49
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50 for o, a in opts:
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51 if o == '-h':
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52 print 'Usage:'
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53 print ' %s <fr-hit_output_file>' % sys.argv[0]
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54 sys.exit(0)
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55 else:
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56 print 'unhandled option'
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57 sys.exit(1)
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58
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59 if len(args) == 0:
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60 print 'Specify an FR-HIT output file as an argument'
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61 sys.exit(1)
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62
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63 for frag in FRHITFile(args[0]):
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64 print frag
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