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#!/usr/bin/env python3
"""
Compare two GFA files
Note: the current version is not yet functional and only checking segments.
Work in progress.
"""
import sys
import os
import gfapy
import argparse
op = argparse.ArgumentParser(description=__doc__)
op.add_argument('--version', action='version', version='%(prog)s 0.1')
op.add_argument("filename1")
op.add_argument("filename2")
opts = op.parse_args()
gfa1 = gfapy.Gfa.from_file(opts.filename1)
gfa2 = gfapy.Gfa.from_file(opts.filename2)
different = False
if gfa1.version != gfa2.version:
print("# different version")
exit(1)
else:
for s in gfa1.segments:
s2 = gfa2.segment(s)
if s2 is None:
different = True
print("# segment {} in {} but not in {}".format(s.name, opts.filename1, opts.filename2))
if s.diff(s2):
different = True
for diff in s.diff(s2):
print(diff)
for s in gfa2.segments:
s1 = gfa1.segment(s)
if s1 is None:
different = True
print("# segment {} in {} but not in {}".format(s.name, opts.filename2, opts.filename1))
if different:
exit(1)
else:
exit(0)
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