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#! /usr/bin/env python3
# Author: Martin C. Frith 2018
from __future__ import print_function
import argparse
import collections
import gzip
import itertools
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):
if sLineFields[4] == "-":
seqLen = int(sLineFields[5])
cutBeg, cutEnd = seqLen - cutEnd, seqLen - cutBeg
beg = int(sLineFields[2])
if beg >= cutEnd:
return 0, 0
span = int(sLineFields[3])
end = beg + span
if end <= cutBeg:
return 0, 0
sequenceWithGaps = sLineFields[6]
monomerLen = (len(sequenceWithGaps) - sequenceWithGaps.count("-")) // span
seqBeg = max(cutBeg - beg, 0) * monomerLen
alnBeg = alnBegFromSeqBeg(sequenceWithGaps, seqBeg)
seqEnd = min(cutEnd - beg, span) * monomerLen
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 sLineCutData(fields, alnBeg, alnEnd):
span = int(fields[3])
seq = fields[6]
n = len(seq)
begSpan = alnBeg - seq.count("-", 0, alnBeg)
endSpan = n - alnEnd - seq.count("-", alnEnd, n)
mul = (n - seq.count("-")) // span
b = begSpan // mul
e = endSpan // mul
return int(fields[2]) + b, span - b - e, begSpan % mul, endSpan % mul
def addMafData(dataPerSeq, mafLines, alnBeg, alnEnd):
for line in mafLines:
if line[0] == "s":
fields = line.split()
seqName = fields[1] # xxx omit theSpecifiedSequence ?
strand = fields[4]
seqLen = int(fields[5])
beg, span, begRem, endRem = sLineCutData(fields, alnBeg, alnEnd)
alnBeg -= begRem
alnEnd += endRem
end = beg + span
if strand == "-":
beg, end = seqLen - end, seqLen - beg
seqData = seqLen, beg, end
dataPerSeq[seqName].append(seqData)
def cutMafRecords(mafLines, alnBeg, alnEnd):
for line in mafLines:
fields = line.split()
if line[0] == "s":
beg, span, begRem, endRem = sLineCutData(fields, alnBeg, alnEnd)
alnBeg -= begRem
alnEnd += endRem
newSeq = fields[6][alnBeg:alnEnd]
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 = zip(*sRecords)
for i in sColumns:
yield max(map(len, i))
def printMafLine(fieldWidths, fields):
formatParams = itertools.chain.from_iterable(zip(fieldWidths, fields))
print("%*s %-*s %*s %*s %*s %*s %*s" % tuple(formatParams))
def printOneMaf(mafRecords):
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 nameFromTitleLine(line):
return line[1:].split()[0]
def doOneFastaSequence(dataPerSeq, topLine, seqLines):
alnData = dataPerSeq.get(nameFromTitleLine(topLine))
if alnData:
seq = "".join(i.rstrip() for i in seqLines)
seqLen = len(seq)
alnData = [i for i in alnData if i[0] == seqLen]
if alnData:
beg = min(i[1] for i in alnData)
end = max(i[2] for i in alnData)
print(topLine, end="")
print(seq[beg:end])
def doOneFastqSequence(dataPerSeq, lines):
alnData = dataPerSeq.get(nameFromTitleLine(lines[0]))
if alnData:
seqLen = len(lines[1].rstrip())
alnData = [i for i in alnData if i[0] == seqLen]
if alnData:
beg = min(i[1] for i in alnData)
end = max(i[2] for i in alnData)
print(lines[0], end="")
print(lines[1][beg:end])
print(lines[2], end="")
print(lines[3][beg:end])
def printFastaParts(dataPerSeq, topLine, lines):
seqLines = []
for line in lines:
if line[0] == ">":
doOneFastaSequence(dataPerSeq, topLine, seqLines)
topLine = line
seqLines = []
else:
seqLines.append(line)
doOneFastaSequence(dataPerSeq, topLine, seqLines)
def printFastqParts(dataPerSeq, topLine, lines):
b = [topLine]
for i, x in enumerate(lines):
b.append(x)
if i % 4 == 2:
doOneFastqSequence(dataPerSeq, b)
b = []
def printSequenceParts(dataPerSeq, lines):
for line in lines:
if line[0] == ">":
printFastaParts(dataPerSeq, line, lines)
elif line[0] == "@":
printFastqParts(dataPerSeq, line, lines)
else:
raise RuntimeError("can't read the sequence data")
break
def cutOneMaf(seqName, cutBeg, cutEnd, dataPerSeq, mafLines):
sLineFields = findTheSpecifiedSequence(seqName, mafLines)
if not sLineFields:
return
alnBeg, alnEnd = alignmentRange(cutBeg, cutEnd, sLineFields)
if alnBeg >= alnEnd:
return
if dataPerSeq is None:
mafRecords = list(cutMafRecords(mafLines, alnBeg, alnEnd))
printOneMaf(mafRecords)
else:
addMafData(dataPerSeq, mafLines, alnBeg, alnEnd)
def wantedRange(cutSpecification):
seqName = None
s = cutSpecification.split()
if len(s) == 3:
seqName, beg, end = s
elif len(s) == 2:
beg, end = s
else:
if ":" in cutSpecification:
seqName, cutSpecification = cutSpecification.rsplit(":", 1)
beg, end = cutSpecification.rsplit("-", 1)
return seqName, int(beg), int(end)
def mafCut(args):
seqName, cutBeg, cutEnd = wantedRange(args.segment)
dataPerSeq = collections.defaultdict(list) if args.sequences else None
mafLines = []
for line in myOpen(args.alignments):
if line.isspace():
cutOneMaf(seqName, cutBeg, cutEnd, dataPerSeq, mafLines)
mafLines = []
elif line[0] != "#":
mafLines.append(line)
cutOneMaf(seqName, cutBeg, cutEnd, dataPerSeq, mafLines)
if dataPerSeq:
for fileName in args.sequences:
printSequenceParts(dataPerSeq, myOpen(fileName))
if __name__ == "__main__":
signal.signal(signal.SIGPIPE, signal.SIG_DFL) # avoid silly error message
description = "Get parts of MAF-format alignments."
ap = argparse.ArgumentParser(description=description)
ap.add_argument("segment",
help="zero-based sequence range, e.g. chr7:123400-123500")
ap.add_argument("alignments", nargs="?", default="-",
help="file of sequence alignments in MAF format")
ap.add_argument("sequences", nargs="*", default=None, # xxx need default?
help="file of sequences in fasta or fastq format")
args = ap.parse_args()
mafCut(args)
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