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#! /usr/bin/python3
# Author: Martin C. Frith 2018
from __future__ import print_function
import gzip
import itertools
import optparse
import signal
import sys
def myOpen(fileName): # faster than fileinput
if fileName == "-":
return sys.stdin
if fileName.endswith(".gz"):
return gzip.open(fileName, "rt") # xxx dubious for Python2
return open(fileName)
def alnBegFromSeqBeg(gappedSequence, seqBeg):
for i, x in enumerate(gappedSequence):
if x != "-":
if seqBeg == 0:
return i
seqBeg -= 1
def alnEndFromSeqEnd(gappedSequence, seqEnd):
for i, x in enumerate(gappedSequence):
if x != "-":
seqEnd -= 1
if seqEnd == 0:
return i + 1
def alignmentRange(cutBeg, cutEnd, sLineFields):
beg = int(sLineFields[2])
if beg >= cutEnd:
return 0, 0
sequenceWithGaps = sLineFields[6]
span = len(sequenceWithGaps) - sequenceWithGaps.count("-")
end = beg + span
if end <= cutBeg:
return 0, 0
seqBeg = max(cutBeg - beg, 0)
alnBeg = alnBegFromSeqBeg(sequenceWithGaps, seqBeg)
seqEnd = min(cutEnd - beg, span)
alnEnd = alnEndFromSeqEnd(sequenceWithGaps, seqEnd)
return alnBeg, alnEnd
def findTheSpecifiedSequence(seqName, mafLines):
for line in mafLines:
if line[0] == "s":
fields = line.split()
if seqName is None or fields[1] == seqName:
return fields
return None
def cutMafRecords(mafLines, alnBeg, alnEnd):
for line in mafLines:
fields = line.split()
if line[0] == "s":
oldSeq = fields[6]
newSeq = oldSeq[alnBeg:alnEnd]
beg = int(fields[2]) + alnBeg - oldSeq[:alnBeg].count("-")
span = len(newSeq) - newSeq.count("-")
yield fields[:2] + [str(beg), str(span)] + fields[4:6] + [newSeq]
elif line[0] == "q":
yield fields[:2] + [fields[2][alnBeg:alnEnd]]
elif line[0] == "p":
yield fields[:1] + [fields[1][alnBeg:alnEnd]]
else:
yield fields
def mafFieldWidths(mafRecords):
sRecords = (i for i in mafRecords if i[0] == "s")
sColumns = list(zip(*sRecords))
for i in sColumns:
yield max(list(map(len, i)))
def printMafLine(fieldWidths, fields):
formatParams = itertools.chain.from_iterable(list(zip(fieldWidths, fields)))
print("%*s %-*s %*s %*s %*s %*s %*s" % tuple(formatParams))
def cutOneMaf(cutRange, mafLines):
seqName, cutBeg, cutEnd = cutRange
sLineFields = findTheSpecifiedSequence(seqName, mafLines)
if not sLineFields:
return
alnBeg, alnEnd = alignmentRange(cutBeg, cutEnd, sLineFields)
if alnBeg >= alnEnd:
return
mafRecords = list(cutMafRecords(mafLines, alnBeg, alnEnd))
fieldWidths = list(mafFieldWidths(mafRecords))
for fields in mafRecords:
if fields[0] == "s":
printMafLine(fieldWidths, fields)
elif fields[0] == "q":
printMafLine(fieldWidths, fields[:2] + [""] * 4 + fields[2:])
elif fields[0] == "p":
printMafLine(fieldWidths, fields[:1] + [""] * 5 + fields[1:])
else:
print(" ".join(fields))
print()
def mafCutOneFile(cutRange, lines):
mafLines = []
for line in lines:
if line.isspace():
cutOneMaf(cutRange, mafLines)
mafLines = []
elif line[0] != "#":
mafLines.append(line)
cutOneMaf(cutRange, mafLines)
def wantedRange(cutSpecification):
seqName = None
if ":" in cutSpecification:
seqName, cutSpecification = cutSpecification.rsplit(":", 1)
beg, end = cutSpecification.rsplit("-", 1)
return seqName, int(beg), int(end)
def mafCut(opts, args):
cutRange = wantedRange(args[0])
if len(args) > 1:
for i in args[1:]:
mafCutOneFile(cutRange, myOpen(i))
else:
mafCutOneFile(cutRange, sys.stdin)
if __name__ == "__main__":
signal.signal(signal.SIGPIPE, signal.SIG_DFL) # avoid silly error message
usage = "%prog chrN:start-end alignments.maf"
description = "Get parts of MAF-format alignments."
op = optparse.OptionParser(usage=usage, description=description)
opts, args = op.parse_args()
if not args:
op.error("please give me a cut specification and MAF alignments")
mafCut(opts, args)
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