def main(argv=None):
parser=argparse.ArgumentParser(description="Pipe out the alignments involving or excluding provided contigs ID")
parser.add_argument('-e',dest="inverse_match",action="store_true",help="Inverse the criterion, filter out any conting in CONTIGID list (not implemented yet)")
parser.add_argument('-r',dest="use_re",action="store_true",help="Consider CONTIGID as python regexp (not implemented yet)")
parser.add_argument('-s',dest="remove_self",action="store_true",help="remove self alignments")
parser.add_argument('-p',dest="pretty",action="store_true",help="Pretty print")
parser.add_argument('-v',dest="verbose",action="store_true",help="Verbose output")
parser.add_argument('infile', nargs='?', type=argparse.FileType('r'), default=sys.stdin)
parser.add_argument('-o', nargs='?', type=argparse.FileType('w'), default=sys.stdout,dest="outfile")
parser.add_argument('CONTIGS',action='append',nargs="+",help='List of CONTIGS to keep. Use "*" to keep them all')
args=parser.parse_args()
contig_ids=args.CONTIGS[0]
alignments=mummerParser.parse_mummerFile(args.infile)
kept_alignments=[]
for a in alignments:
if "*" in contig_ids and ((args.remove_self and a['TAGQ']!=a['TAGR'])or not args.remove_self):
kept_alignments.append(a)
if a['TAGQ'] in contig_ids and a['TAGR'] in contig_ids:
kept_alignments.append(a)
elif args.verbose:
print >>args.outfile,"Skipped",a
for a in kept_alignments:
mummerParser.print_alignment(a,args.outfile,args.pretty)
def is_kept(aln): idy_threshold = 75 #98 cov_threshold = 99 #95 aln_threshold = 125 ctg_threshold= 0 # skip self if aln['TAGQ']==aln['TAGR']: return False # Skip under threshold threshold_aln_OK = (int(aln["LEN1"]) > aln_threshold and int(aln["LEN2"]) > aln_threshold) threshold_ctg_OK = (int(aln["LENR"]) > ctg_threshold and int(aln["LENQ"]) > ctg_threshold) if (not threshold_ctg_OK) or (not threshold_aln_OK): return False A1, A2 = get_assembler_name (aln["TAGR"]), get_assembler_name (aln["TAGQ"]) if (A1==A2): return False # if (aln["TAGR"] != aln["TAGQ"]) and ((aln["COVR"] > cov_threshold) or ((aln["LENR"] - aln["LEN1"]) < ctg_threshold)): # return False # elif (aln["TAGR"] != aln["TAGQ"]) and ((aln["COVQ"] > cov_threshold) or ((aln["LENQ"] - aln["LEN2"]) < ctg_threshold)): # return False if (aln["TAGR"] != aln["TAGQ"]) and (aln["IDY"] > idy_threshold) and threshold_aln_OK and threshold_ctg_OK and (A1 != A2): return True else: return False mummerParser.print_alignment(aln,sys.stderr,pretty=True) assert(False)
def is_kept(aln):
idy_threshold = 75 #98
cov_threshold = 99 #95
aln_threshold = 125
ctg_threshold = 0
# skip self
if aln['TAGQ'] == aln['TAGR']:
return False
# Skip under threshold
threshold_aln_OK = (int(aln["LEN1"]) > aln_threshold
and int(aln["LEN2"]) > aln_threshold)
threshold_ctg_OK = (int(aln["LENR"]) > ctg_threshold
and int(aln["LENQ"]) > ctg_threshold)
if (not threshold_ctg_OK) or (not threshold_aln_OK):
return False
A1, A2 = get_assembler_name(aln["TAGR"]), get_assembler_name(aln["TAGQ"])
if (A1 == A2):
return False
# if (aln["TAGR"] != aln["TAGQ"]) and ((aln["COVR"] > cov_threshold) or ((aln["LENR"] - aln["LEN1"]) < ctg_threshold)):
# return False
# elif (aln["TAGR"] != aln["TAGQ"]) and ((aln["COVQ"] > cov_threshold) or ((aln["LENQ"] - aln["LEN2"]) < ctg_threshold)):
# return False
if (aln["TAGR"] != aln["TAGQ"]) and (
aln["IDY"] > idy_threshold
) and threshold_aln_OK and threshold_ctg_OK and (A1 != A2):
return True
else:
return False
mummerParser.print_alignment(aln, sys.stderr, pretty=True)
assert (False)
def main(argv=None):
parser = argparse.ArgumentParser(
description=
"Pipe out the alignments involving or excluding provided contigs ID")
parser.add_argument(
'-e',
dest="inverse_match",
action="store_true",
help=
"Inverse the criterion, filter out any conting in CONTIGID list (not implemented yet)"
)
parser.add_argument(
'-r',
dest="use_re",
action="store_true",
help="Consider CONTIGID as python regexp (not implemented yet)")
parser.add_argument('-s',
dest="remove_self",
action="store_true",
help="remove self alignments")
parser.add_argument('-p',
dest="pretty",
action="store_true",
help="Pretty print")
parser.add_argument('-v',
dest="verbose",
action="store_true",
help="Verbose output")
parser.add_argument('infile',
nargs='?',
type=argparse.FileType('r'),
default=sys.stdin)
parser.add_argument('-o',
nargs='?',
type=argparse.FileType('w'),
default=sys.stdout,
dest="outfile")
parser.add_argument(
'CONTIGS',
action='append',
nargs="+",
help='List of CONTIGS to keep. Use "*" to keep them all')
args = parser.parse_args()
contig_ids = args.CONTIGS[0]
alignments = mummerParser.parse_mummerFile(args.infile)
kept_alignments = []
for a in alignments:
if "*" in contig_ids and ((args.remove_self and a['TAGQ'] != a['TAGR'])
or not args.remove_self):
kept_alignments.append(a)
if a['TAGQ'] in contig_ids and a['TAGR'] in contig_ids:
kept_alignments.append(a)
elif args.verbose:
print >> args.outfile, "Skipped", a
for a in kept_alignments:
mummerParser.print_alignment(a, args.outfile, args.pretty)
