--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FRHIT_parser.py	Tue Dec 02 19:54:00 2014 -0500
@@ -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