| Previous changeset 3:451df50fb4d4 (2014-12-02) Next changeset 5:70e76f6bfcfb (2014-12-02) |
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Commit message:
Uploaded |
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added:
FRHIT_parser.py |
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| diff -r 451df50fb4d4 -r 398c3753c358 FRHIT_parser.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FRHIT_parser.py Tue Dec 02 19:54:00 2014 -0500 |
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| @@ -0,0 +1,64 @@ +#!/usr/bin/env python +""" +Parse the FR-HIT output file format. +""" + +from __future__ import division +import sys, getopt + +class FRHITFragment: + """ + Represents a fragment match to a reference genome. + """ + + def __init__(self, frhit_string): + fields = frhit_string.rstrip().split() + + self.name = fields[0] + self.refseq = fields[8].split('|')[3] + self.location = int(fields[9]) + self.identity = float(fields[7][:-1]) + self.length = int(fields[3]) + + def __repr__(self): + out = [] + out.append("Name: %s\n" % self.name) + out.append("Location: %d\n" % self.location) + out.append("Identity: %4.1f\n" % self.identity) + return ''.join(out) + + +def FRHITFile(filename): + """ + Parses the fr-hit format file, returning FRHITFragment objects. + + This is a generator, so that there is no need to store a full list of + fragments in memory if it's not necessary to do so. + """ + + f = open(filename, 'rb') + + for line in f: + yield FRHITFragment(line) + + f.close() + + +if __name__ == '__main__': + opts, args = getopt.getopt(sys.argv[1:], 'h') + + for o, a in opts: + if o == '-h': + print 'Usage:' + print ' %s <fr-hit_output_file>' % sys.argv[0] + sys.exit(0) + else: + print 'unhandled option' + sys.exit(1) + + if len(args) == 0: + print 'Specify an FR-HIT output file as an argument' + sys.exit(1) + + for frag in FRHITFile(args[0]): + print frag |