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#!/usr/bin/env python
"""
Compare two gfa files, reporting differences but ignoring some trivial ones
---------------------------------------------------------------------------
:Author: Bob Harris (rsharris@bx.psu.edu)
"""
import sys,re
def usage(s=None):
message = """
gfa_compare [--sort] gfa_file1 gfa_file2
"""
if (s == None): sys.exit (message)
else: sys.exit ("%s\n%s" % (s,message))
def main():
# parse the command line
sortEm = False
if (sys.argv[1] == "--sort"):
sortEm = True
del sys.argv[1]
if (len(sys.argv) < 3):
usage("you must specify two gfa files")
elif (len(sys.argv) > 3):
usage("wrong number of arguments")
gfa1Filename = sys.argv[1]
gfa2Filename = sys.argv[2]
# compare the files
gfa1 = file(gfa1Filename,"rt")
gfa2 = file(gfa2Filename,"rt")
if (sortEm): (different,lineNum) = compare_unsorted_files(gfa1,gfa2)
else: (different,lineNum) = compare_sorted_files (gfa1,gfa2)
if (different):
print >>sys.stderr,"FAILURE: %s and %s are different (line %d)" \
% (gfa1Filename,gfa2Filename,lineNum)
sys.exit(1)
print >>sys.stderr,"SUCCESS: %s and %s are equivalent" \
% (gfa1Filename,gfa2Filename)
# compare files that we expect are in the same order
def compare_sorted_files(gfa1,gfa2):
lineNum = 0
while (True):
lineNum += 1
line1 = gfa1.readline()
line2 = gfa2.readline()
if (line1 == "") and (line2 == ""):
return (False,lineNum)
line1 = line1.rstrip()
line2 = line2.rstrip()
stanza = line1.split()[0]
stanza2 = line2.split()[0]
if (stanza2 != stanza):
return (True,lineNum)
if (stanza == "d"):
continue # ignore command line differences
elif (stanza == "h"):
line1 = " ".join(header_strip(line1))
line2 = " ".join(header_strip(line2))
if (line1 != line2):
# print >>sys.stderr,"%s\n%s" % (line1,line2)
return (True,lineNum)
# compare files that we suspect might not be in the same order
def compare_unsorted_files(gfa1,gfa2):
lines1 = read_lines(gfa1)
lines1.sort()
lines2 = read_lines(gfa2)
lines2.sort()
compareNum = 0
while (True):
if (compareNum < len(lines1)): (line1,lineNum1) = lines1[compareNum]
else: (line1,lineNum1) = ("",None)
if (compareNum < len(lines2)): (line2,lineNum2) = lines2[compareNum]
else: (line2,lineNum2) = ("",None)
compareNum += 1
if (line1 == "") and (line2 == ""):
return (False,compareNum)
stanza = line1.split()[0]
stanza2 = line2.split()[0]
if (stanza2 != stanza):
return (True,compareNum)
if (stanza == "d"):
continue # ignore command line differences
elif (stanza == "h"):
line1 = " ".join(header_strip(line1))
line2 = " ".join(header_strip(line2))
if (line1 != line2):
# print >>sys.stderr,"%s\n%s" % (line1,line2)
return (True,compareNum)
# read all lines from a file, a return a list of (line,lineNumber)
def read_lines(gfa):
lines = []
lineNum = 0
while (True):
lineNum += 1
line = gfa.readline()
if (line == ""):
break
lines += [(line.rstrip(),lineNum)]
return lines
headerRe = re.compile("^(?P<stanza>.+) +\"(?P<name1>.+)\" +\"(?P<name2>.+)\"$")
def header_strip(s):
m = headerRe.match(s)
if (m == None):
return s
stanza = m.group("stanza")
name1 = m.group("name1").strip()
name2 = m.group("name2").strip()
if (name1.startswith(">")): name1 = name1[1:].strip()
if (name2.startswith(">")): name2 = name2[1:].strip()
return [stanza,name1,name2]
if __name__ == "__main__": main()
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