def trimMatchOverlapsInBoth(inpfile,outfile,trim_subtype):
gp = MyFile.myfile()
MatchRecord.sortInXorderAP(inpfile,gp)
# The following coalescing assumes perfect runs.
hp = MyFile.myfile()
coalesceMatches( gp, hp, ((trim_subtype == 'x') or (trim_subtype == 'u')) )
gp = MyFile.myfile()
trimMatchOverlapsInX(hp,gp,trim_subtype)
hp = MyFile.myfile()
MatchRecord.sortInYorderAP(gp,hp)
trimMatchOverlapsInY(hp,outfile,trim_subtype)
return
def trimMatchOverlapsInBoth(inpfile, outfile, trim_subtype):
gp = MyFile.myfile()
MatchRecord.sortInXorderAP(inpfile, gp)
# The following coalescing assumes perfect runs.
hp = MyFile.myfile()
coalesceMatches(gp, hp, ((trim_subtype == 'x') or (trim_subtype == 'u')))
gp = MyFile.myfile()
trimMatchOverlapsInX(hp, gp, trim_subtype)
hp = MyFile.myfile()
MatchRecord.sortInYorderAP(gp, hp)
trimMatchOverlapsInY(hp, outfile, trim_subtype)
return
def applyBothKeepMasks(inpfile, outfile):
# Maybe we can think of a masking implementation where each ATAC match
# is treated atomicly. Assume that the keep mask intervals are sorted
# by start postition. Assume that the ATAC matches are sorted by start
# postion. Assert that all keep mask intervals are non-overlapping and
# were cut from only one ATAC match. Thus the mapping from keep mask
# intervals is a function. Note that this requires that we do not
# coalesce abutting keep mask intervals that originate from multiple
# matches. Note this still allows an ATAC match to overlap more than
# one keep mask interval. Ignore all keep mask intervals with zero
# length their creation has tie breaking problems. See notes on 2003
# Jul 29.
debug = 0
debugnum = 0
inpfile.seek(0)
outfile.seek(0)
# Apply the keepMask for the first axis.
# Make the sorted the keep mask intervals for the first axis.
processFirstAxis = 1
keepMaskFile = MyFile.myfile()
tmpfile2 = inpfile
tmpfile3 = MyFile.myfile()
tmpfile4 = MyFile.myfile()
findCoverageIntervals(inpfile, keepMaskFile, processFirstAxis)
if debug:
debugnum += 1
debugfile = open("debugfile.%d" % debugnum, "w")
for line in keepMaskFile:
print >> debugfile, line,
MatchRecord.sortInXorderAP(tmpfile2, tmpfile3)
if debug:
#tmpfile2.seek(0)
#debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
#for line in tmpfile2: print >>debugfile, line,
tmpfile3.seek(0)
debugnum += 1
debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile3:
print >> debugfile, line,
applyOneKeepMask(tmpfile3, tmpfile4, keepMaskFile, processFirstAxis)
if debug:
tmpfile4.seek(0)
debugnum += 1
debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile4:
print >> debugfile, line,
# Apply the keepMask for the second axis.
# Make the sorted the keep mask intervals for the second axis.
processFirstAxis = 0
keepMaskFile = MyFile.myfile()
tmpfile2 = tmpfile4
tmpfile3 = MyFile.myfile()
tmpfile4 = outfile
findCoverageIntervals(inpfile, keepMaskFile, processFirstAxis)
if debug:
debugnum += 1
debugfile = open("debugfile.%d" % debugnum, "w")
for line in keepMaskFile:
print >> debugfile, line,
MatchRecord.sortInYorderAP(tmpfile2, tmpfile3)
if debug:
#tmpfile2.seek(0)
#debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
#for line in tmpfile2: print >>debugfile, line,
tmpfile3.seek(0)
debugnum += 1
debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile3:
print >> debugfile, line,
applyOneKeepMask(tmpfile3, tmpfile4, keepMaskFile, processFirstAxis)
if debug:
tmpfile4.seek(0)
debugnum += 1
debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile4:
print >> debugfile, line,
def applyBothKeepMasks( inpfile, outfile ):
# Maybe we can think of a masking implementation where each ATAC match
# is treated atomicly. Assume that the keep mask intervals are sorted
# by start postition. Assume that the ATAC matches are sorted by start
# postion. Assert that all keep mask intervals are non-overlapping and
# were cut from only one ATAC match. Thus the mapping from keep mask
# intervals is a function. Note that this requires that we do not
# coalesce abutting keep mask intervals that originate from multiple
# matches. Note this still allows an ATAC match to overlap more than
# one keep mask interval. Ignore all keep mask intervals with zero
# length their creation has tie breaking problems. See notes on 2003
# Jul 29.
debug = 0
debugnum = 0
inpfile.seek(0)
outfile.seek(0)
# Apply the keepMask for the first axis.
# Make the sorted the keep mask intervals for the first axis.
processFirstAxis = 1
keepMaskFile = MyFile.myfile()
tmpfile2 = inpfile
tmpfile3 = MyFile.myfile()
tmpfile4 = MyFile.myfile()
findCoverageIntervals( inpfile, keepMaskFile, processFirstAxis)
if debug:
debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
for line in keepMaskFile: print >>debugfile, line,
MatchRecord.sortInXorderAP(tmpfile2,tmpfile3)
if debug:
#tmpfile2.seek(0)
#debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
#for line in tmpfile2: print >>debugfile, line,
tmpfile3.seek(0)
debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile3: print >>debugfile, line,
applyOneKeepMask( tmpfile3, tmpfile4, keepMaskFile, processFirstAxis)
if debug:
tmpfile4.seek(0)
debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile4: print >>debugfile, line,
# Apply the keepMask for the second axis.
# Make the sorted the keep mask intervals for the second axis.
processFirstAxis = 0
keepMaskFile = MyFile.myfile()
tmpfile2 = tmpfile4
tmpfile3 = MyFile.myfile()
tmpfile4 = outfile
findCoverageIntervals( inpfile, keepMaskFile, processFirstAxis)
if debug:
debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
for line in keepMaskFile: print >>debugfile, line,
MatchRecord.sortInYorderAP(tmpfile2,tmpfile3)
if debug:
#tmpfile2.seek(0)
#debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
#for line in tmpfile2: print >>debugfile, line,
tmpfile3.seek(0)
debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile3: print >>debugfile, line,
applyOneKeepMask( tmpfile3, tmpfile4, keepMaskFile, processFirstAxis)
if debug:
tmpfile4.seek(0)
debugnum += 1; debugfile = open("debugfile.%d" % debugnum, "w")
for line in tmpfile4: print >>debugfile, line,
