def main():
# parse the command line
headLimit = None
requireEof = True
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=", 1)[1]
if (arg.startswith("--head=")):
headLimit = int_with_unit(argVal)
elif (arg in ["--noendmark", "--noeof", "--nomark"]): # (unadvertised)
requireEof = False
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
alignmentNum = 0
for a in alignments(stdin, requireEof):
alignmentNum += 1
if (headLimit != None) and (alignmentNum > headLimit):
print >> stderr, "limit of %d alignments reached" % headLimit
break
positionalStats = a.positional_stats()
numPositions = len(positionalStats)
vec = [None] * (2 * numPositions + 1)
vec[0] = a.lineNumber
for (pos, stats) in enumerate(positionalStats):
if ("m" not in stats):
raise ValueError, \
"\"m\" missing from positional information for alignment at line %d" \
% a.lineNumber
if ("x" not in stats):
raise ValueError, \
"\"x\" missing from positional information for alignment at line %d" \
% a.lineNumber
vec[1 + pos] = stats["m"]
vec[1 + numPositions + pos] = stats["x"]
print "\t".join(map(str, vec))
def main():
# parse the command line
minMRatio = None
requireEof = True
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=",1)[1]
if (arg.startswith("--minmratio=")):
minMRatio = parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit("%s: mratio has to be between 0 and 1 (e.g. 0.85 or 85%%)\n%s"
% (os_path.basename(argv[0]),arg))
elif (arg.startswith("--maxnoise=")):
minMRatio = 1 - parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit("%s: noise has to be between 0 and 1 (e.g. 0.15 or 15%%)\n%s"
% (os_path.basename(argv[0]),arg))
elif (arg in ["--noendmark","--noeof","--nomark"]): # (unadvertised)
requireEof = False
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
print "\t".join(["#line","seq","strand","start","end","querybp","mRatio","nErrors","errors"])
for a in alignments(stdin,requireEof):
if (minMRatio != None) and (a.mRatio < minMRatio):
continue
errorPositions = []
for (ix,ch) in enumerate(a.errorText):
if (ch == "x"):
errorPositions += [float(ix)/(len(a.errorText)-1)]
print "\t".join([str(a.lineNumber),
a.seqName,a.strand,str(a.start),str(a.end),
str(a.motifBaseCount),
"%.1f%%" % (100*a.mRatio),
str(len(errorPositions))]
+ map(lambda x:"%.3f"%x,errorPositions))
def collect_alignments(f,
testWhich,
headLimit=None,
subsampleK=None,
subsampleN=None,
requireEof=True):
alignmentList = []
mxMatrix = []
unitLength = None
alignmentNum = 0
for a in alignments(f, requireEof):
alignmentNum += 1
if (reportProgress != None) \
and ((alignmentNum == 1) or (alignmentNum % reportProgress == 0)):
print >>stderr, "progress: reading alignment %s" \
% (commatize(alignmentNum))
if (headLimit != None) and (alignmentNum > headLimit):
print >> stderr, "limit of %d alignments reached" % headLimit
break
if (subsampleN != None):
if ((alignmentNum - 1) % subsampleN != (subsampleK - 1)): continue
if (testWhich == "matches-insertions"):
# note [1]
mxRow = positional_error_vector(a, modified="m-i")
else:
mxRow = positional_error_vector(a)
if (mxRow == None):
raise ValueError, \
"alignment at line %d does not contain positional information" \
% a.lineNumber
if (unitLength == None):
unitLength = len(mxRow) / 2
elif (len(mxRow) != 2 * unitLength):
raise ValueError, \
"alignments have different motif lengths, %d and %d (detected at line %d)" \
% (unitLength,len(mxRow)/2,a.lineNumber)
alignmentList += [a]
mxMatrix += [mxRow]
return (unitLength, alignmentList, mxMatrix)
def main():
# parse the command line
minMRatio = None
requireEof = True
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=", 1)[1]
if (arg.startswith("--minmratio=")):
minMRatio = parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit(
"%s: mratio has to be between 0 and 1 (e.g. 0.85 or 85%%)\n%s"
% (os_path.basename(argv[0]), arg))
elif (arg.startswith("--maxnoise=")):
minMRatio = 1 - parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit(
"%s: noise has to be between 0 and 1 (e.g. 0.15 or 15%%)\n%s"
% (os_path.basename(argv[0]), arg))
elif (arg in ["--noendmark", "--noeof", "--nomark"]): # (unadvertised)
requireEof = False
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
for a in alignments(stdin, requireEof):
if (minMRatio != None) and (a.mRatio < minMRatio):
continue
print "\t".join([
a.seqName,
str(a.start),
str(a.end), ".",
"%d" % (1000 * a.mRatio), a.strand
])
def main():
global debug
# parse the command line
countRatio = 1
headLimit = None
requireEof = True
debug = []
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=", 1)[1]
if (arg.startswith("--minwordratio=")) or (
arg.startswith("--ratio=")) or (arg.startswith("R=")):
countRatio = float_or_fraction(argVal)
elif (arg.startswith("--head=")):
headLimit = int_with_unit(argVal)
elif (arg in ["--noendmark", "--noeof", "--nomark"]): # (unadvertised)
requireEof = False
elif (arg == "--debug"):
debug += ["debug"]
elif (arg.startswith("--debug=")):
debug += argVal.split(",")
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
alignmentNum = 0
for a in alignments(stdin, requireEof):
alignmentNum += 1
if (headLimit != None) and (alignmentNum > headLimit):
print >> stderr, "limit of %d alignments reached" % headLimit
break
if (alignmentNum > 1): print
print "\n".join(a.lines)
motifText = a.motifText
seqText = a.seqText
if ("noflip" in debug):
pass
elif (a.strand == "-") and (a.start < a.end):
# alignment was reported in reverse complement of motif, so flip it
motifText = reverse_complement(motifText)
seqText = reverse_complement(seqText)
(motifChunks, seqChunks) = chunkify(a.motif, motifText, seqText)
wordCounts = Counter()
for word in seqChunks:
word = word.replace("-", "")
if (word != a.motif): word = word.lower()
wordCounts[word] += 1
if (a.motif in wordCounts): motifCount = wordCounts[a.motif]
else: motifCount = 0
wordCounts = [(wordCounts[word], abs(len(word) - len(a.motif)), word)
for word in wordCounts
if (wordCounts[word] >= motifCount * countRatio)]
wordCounts.sort()
wordCounts.reverse()
print "# aligned words %s" % \
" ".join(["%s:%d"%(word,count) for (count,_,word) in wordCounts])
if ("chunks" in debug):
if ("noflip" in debug):
seqChunks = [
reverse_complement(word) for word in seqChunks[::-1]
]
motifChunks = [
reverse_complement(word) for word in motifChunks[::-1]
]
print "# words: %s" % " ".join(seqChunks)
print "# motif: %s" % " ".join(motifChunks)
if (requireEof):
print "# ncrf end-of-file"
def main():
# parse the command line
minMRatio = None
requireEof = True
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=", 1)[1]
if (arg.startswith("--minmratio=")):
minMRatio = parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit(
"%s: mratio has to be between 0 and 1 (e.g. 0.85 or 85%%)\n%s"
% (os_path.basename(argv[0]), arg))
elif (arg.startswith("--maxnoise=")):
minMRatio = 1 - parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit(
"%s: noise has to be between 0 and 1 (e.g. 0.15 or 15%%)\n%s"
% (os_path.basename(argv[0]), arg))
elif (arg in ["--noendmark", "--noeof", "--nomark"]): # (unadvertised)
requireEof = False
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
print "\t".join([
"#line", "motif", "seq", "start", "end", "strand", "seqLen", "querybp",
"consensus"
])
userHasntBeenWarned = True
for a in alignments(stdin, requireEof):
seqLenStr = "NA"
if (a.seqLen != None):
seqLenStr = str(a.seqLen)
if (hasattr(a, "mRatio")):
if (minMRatio != None) and (a.mRatio < minMRatio):
continue
consensuses = []
for line in a.lines:
if (not line.startswith("# consensus")): continue
line = line.split(None, 2)
consensuses += [line[2]]
if (consensuses == []):
if (userHasntBeenWarned):
print >>stderr, \
("WARNING: input alignments did not contain a consensus line"
+ "\n (ncrf_consensus_filter would create that line)")
userHasntBeenWarned = False
consensus = "(missing)"
else:
consensus = ",".join(consensuses)
print "\t".join([
str(a.lineNumber), a.motif, a.seqName,
str(a.start),
str(a.end), a.strand, seqLenStr,
str(a.motifBaseCount), consensus
])
def main():
# parse the command line
writeHeader = False
writeWhat = "per alignment"
headLimit = None
requireEof = True
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=",1)[1]
if (arg in ["--withheader","--with=header","--with:header"]):
writeHeader = True
elif (arg in ["--sumonly","--sum=only","--sum:only"]):
writeWhat = "sum only"
elif (arg.startswith("--head=")):
headLimit = int_with_unit(argVal)
elif (arg in ["--noendmark","--noeof","--nomark"]): # (unadvertised)
requireEof = False
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
sum = {"m":0, "mm":0, "io":0, "ix":0, "do":0, "dx":0}
alignmentNum = 0
for a in alignments(stdin,requireEof):
alignmentNum +=1
if (headLimit != None) and (alignmentNum > headLimit):
print >>stderr, "limit of %d alignments reached" % headLimit
break
(nMatch,nMismatch,nInsO,nInsX,nDelO,nDelX) = extract_events(a)
if (writeHeader):
print "\t".join(["line","motif","mRatio","m","mm","io","ix","do","dx"])
writeHeader = False
if (writeWhat == "per alignment"):
vec = [a.lineNumber,a.motif,a.mRatio,nMatch,nMismatch,nInsO,nInsX,nDelO,nDelX]
print "\t".join(map(str,vec))
sum["m"] += nMatch
sum["mm"] += nMismatch
sum["io"] += nInsO
sum["ix"] += nInsX
sum["do"] += nDelO
sum["dx"] += nDelX
sum["events"] = (sum["m"] + sum["mm"] + sum["io"] + sum["ix"] + sum["do"] + sum["dx"])
if (alignmentNum == 0):
print >>stderr, "WARNING: input contained no alignments"
elif (writeWhat == "sum only"):
mRatio = float(sum["m"]) / sum["events"]
mRatio = "%.3f" % mRatio
vec = ["all",a.motif,mRatio,sum["m"],sum["mm"],sum["io"],sum["ix"],sum["do"],sum["dx"]]
print "\t".join(map(str,vec))
def main():
# parse the command line
minMRatio = None
requireEof = True
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=",1)[1]
if (arg.startswith("--minmratio=")):
minMRatio = parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit("%s: mratio has to be between 0 and 1 (e.g. 0.85 or 85%%)\n%s"
% (os_path.basename(argv[0]),arg))
elif (arg.startswith("--maxnoise=")):
minMRatio = 1 - parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit("%s: noise has to be between 0 and 1 (e.g. 0.15 or 15%%)\n%s"
% (os_path.basename(argv[0]),arg))
elif (arg in ["--noendmark","--noeof","--nomark"]): # (unadvertised)
requireEof = False
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
print "\t".join(["#line","motif",
"seq","start","end","strand",
"seqLen","querybp",
"mRatio","m","mm","i","d"])
userHasntBeenWarned = True
for a in alignments(stdin,requireEof):
seqLenStr = "NA"
mRatioStr = "NA"
nMatchStr = "NA"
nMismatchStr = "NA"
nInsertionsStr = "NA"
nDeletionsStr = "NA"
if (a.seqLen != None):
seqLenStr = str(a.seqLen)
if (hasattr(a,"mRatio")):
if (minMRatio != None) and (a.mRatio < minMRatio):
continue
mRatioStr = "%.1f%%" % (100*a.mRatio)
if (hasattr(a,"nMatch")):
nMatchStr = str(a.nMatch)
if (hasattr(a,"nMismatch")):
nMismatchStr = str(a.nMismatch)
if (hasattr(a,"nInsertions")):
nInsertionsStr = str(a.nInsertions)
if (hasattr(a,"nDeletions")):
nDeletionsStr = str(a.nDeletions)
if (mRatioStr == "NA"):
if (userHasntBeenWarned):
print >>stderr, \
("WARNING: input alignments did not contain an event stats line"
+ "\n (NCRF --stats=events would create that line)")
userHasntBeenWarned = False
print "\t".join([str(a.lineNumber),
a.motif,
a.seqName,str(a.start),str(a.end),a.strand,
seqLenStr,str(a.motifBaseCount),
mRatioStr,
nMatchStr,nMismatchStr,nInsertionsStr,nDeletionsStr])
def main():
global debug
# parse the command line
maxMRatio = 0.85
minColumns = 10
headLimit = None
reportClumps = False
requireEof = True
debug = []
for arg in argv[1:]:
if ("=" in arg):
argVal = arg.split("=",1)[1]
if (arg.startswith("--maxMRatio=")):
maxMRatio = parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit("%s: mratio has to be between 0 and 1 (e.g. 0.85 or 85%%)\n%s"
% (os_path.basename(argv[0]),arg))
elif (arg.startswith("--minnoise=")):
maxMRatio = 1 - parse_noise_rate(argVal)
if (not (0.0 <= minMRatio <= 1.0)):
exit("%s: noise has to be between 0 and 1 (e.g. 0.15 or 15%%)\n%s"
% (os_path.basename(argv[0]),arg))
elif (arg.startswith("--mincolumns=")) or (arg.startswith("--mindenom=")):
minColumns =int(argVal)
if (minColumns < 2):
usage("minimum length has to be at least two columns\n%s" % arg)
elif (arg.startswith("--head=")):
headLimit = int_with_unit(argVal)
elif (arg == "--report:clumps") or (arg == "--report=clumps"):
reportClumps = True
elif (arg in ["--noendmark","--noeof","--nomark"]): # (unadvertised)
requireEof = False
elif (arg == "--debug"):
debug += ["debug"]
elif (arg.startswith("--debug=")):
debug += argVal.split(",")
elif (arg.startswith("--")):
usage("unrecognized option: %s" % arg)
else:
usage("unrecognized option: %s" % arg)
# process the alignments
alignmentNum = 0
for a in alignments(stdin,requireEof):
alignmentNum +=1
if (headLimit != None) and (alignmentNum > headLimit):
print >>stderr, "limit of %d alignments reached" % headLimit
break
if (a.errorText == None):
exit("%s: alignment at line %d doesn't include error text"
% (os_path.basename(argv[0]),a.lineNumber))
if ("detail" in debug):
print >>stderr, "\nlooking for clumps in %s %c %u-%u" \
% (a.seqName,a.strand,a.start,a.end)
clumps = find_clumps(a.errorText,1-maxMRatio,minColumns,
positiveCh='x',negativeCh='=')
clumpText = ["-"] * len(a.errorText)
for (start,end) in clumps:
for ix in xrange(start,end): clumpText[ix] = "*"
clumpText = "".join(clumpText)
prefixLen = 1 + a.lines[0].find(" =")
if (prefixLen < 0):
prefixLen = 1 + a.lines[0].find(" x")
if (alignmentNum > 1): print
a.lines.insert(3,"# %-*s%s" % (prefixLen-2,"noise clumps",clumpText))
print a
if (reportClumps):
for (start,end) in clumps:
errorCount = matchCount = 0
for ch in a.errorText[start:end]:
if (ch == 'x'): errorCount += 1
elif (ch == '='): matchCount += 1
print >>stderr, "line %d (%d,%d) m=%s x=%s mRatio: %.2f%%" \
% (a.lineNumber,
start,end,matchCount,errorCount,
(100.0*matchCount)/(matchCount+errorCount))
if (requireEof):
print "# ncrf end-of-file"
def sliced_consensus_filter(f, motifsOfInterest, nameToMotif, sliceWidth,
sliceStep):
global userHasBeenWarned
if (reportMsa) and (not userHasBeenWarned):
print >> stderr, "WARNING: sliced consensus doesn't report MSA, ignoring that request"
userHasBeenWarned = True
alignmentNum = 0
alignmentsWritten = 0
for a in alignments(f, requireEof):
alignmentNum += 1
if (reportProgress != None):
if (alignmentNum == 1) or (alignmentNum % reportProgress == 0):
print >>stderr, "progress: testing alignment %s" \
% commatize(alignmentNum)
if (headLimit != None) and (alignmentNum > headLimit):
print >> stderr, "limit of %d alignments reached" % headLimit
break
if (a.motif in nameToMotif):
a.motif = nameToMotif[a.motif]
if (motifsOfInterest != None) and (a.motif not in motifsOfInterest):
continue
if ([ch for ch in a.motif if (ch not in "ACGT")] != []):
abort_warn_about_named_motifs(a)
motifText = a.motifText
seqText = a.seqText
if ("noflip" in debug):
pass
elif (a.strand == "-") and (a.start < a.end):
# alignment was reported in reverse complement of motif, so flip it
motifText = reverse_complement(motifText)
seqText = reverse_complement(seqText)
# look for consensus over each slice, separately
consensuses = set()
numSlices = (len(motifText) + sliceStep -
1) / sliceStep # (an overestimate)
minSlice = 10 * len(a.motif)
for sliceNum in xrange(numSlices):
sliceStart = sliceNum * sliceStep
sliceEnd = min(sliceStart + sliceWidth, len(motifText))
if (sliceEnd - sliceStart < minSlice): break
motifTextSlice = motifText[sliceStart:sliceEnd]
seqTextSlice = seqText[sliceStart:sliceEnd]
# derive consensus(es)
seqChunks = chunkify(a.motif, motifTextSlice, seqTextSlice)
if ("consensus" in debug):
print >> stderr
print >>stderr, "%d score=%d slice.start=%d slice.end=%d" \
% (a.lineNumber,a.score,sliceStart,sliceEnd)
sliceConsensuses = derive_consensuses(
seqChunks, winnerThreshold=winnerThreshold)
sliceConsensuses = list(sliceConsensuses)
if (sliceConsensuses == []):
consensuses.add(None)
else:
for word in sliceConsensuses:
consensuses.add(word)
if ("consensus" in debug):
for word in sliceConsensuses:
print >> stderr, "consensus %s" % word
consensuses = list(consensuses)
# discard the alignment if it meets the filtering criterion (if there
# is any such criterion)
if (filterToKeep == "consensus"):
if (a.motif not in consensuses): continue # (discard it)
elif (filterToKeep == "non consensus"):
if (a.motif in consensuses): continue # (discard it)
else: # if (filterToKeep == "no filter"):
pass
# copy the (unfiltered) alignment to the output
if (alignmentsWritten > 0): print
alignmentsWritten += 1
print "\n".join(a.lines)
# report the consensus, if we're supposed to
if (reportConsensus):
if (consensuses == []):
print "# consensus (none)"
else:
canonicalized = []
for motif in consensuses:
if (motif == None): continue
if (motif != a.motif) and (canonicalizeConsensuses):
(motif, strand) = canonical_motif(motif)
canonicalized += [motif]
if (None in consensuses):
canonicalized += ["(none)"]
print "# consensus %s" % ",".join(canonicalized)
if (requireEof):
print "# ncrf end-of-file"
def simple_consensus_filter(f, motifsOfInterest, nameToMotif):
alignmentNum = 0
alignmentsWritten = 0
for a in alignments(f, requireEof):
alignmentNum += 1
if (reportProgress != None):
if (alignmentNum == 1) or (alignmentNum % reportProgress == 0):
print >>stderr, "progress: testing alignment %s" \
% commatize(alignmentNum)
if (headLimit != None) and (alignmentNum > headLimit):
print >> stderr, "limit of %d alignments reached" % headLimit
break
if (a.motif in nameToMotif):
a.motif = nameToMotif[a.motif]
if (motifsOfInterest != None) and (a.motif not in motifsOfInterest):
continue
if ([ch for ch in a.motif if (ch not in "ACGT")] != []):
abort_warn_about_named_motifs(a)
motifText = a.motifText
seqText = a.seqText
if ("noflip" in debug):
pass
elif (a.strand == "-") and (a.start < a.end):
# alignment was reported in reverse complement of motif, so flip it
motifText = reverse_complement(motifText)
seqText = reverse_complement(seqText)
# derive consensus(es)
seqChunks = chunkify(a.motif, motifText, seqText)
if ("consensus" in debug):
print >> stderr
print >> stderr, "%d score=%d" % (a.lineNumber, a.score)
consensuses = derive_consensuses(seqChunks,
winnerThreshold=winnerThreshold)
consensuses = list(consensuses)
# discard the alignment if it meets the filtering criterion (if there
# is any such criterion)
if (filterToKeep == "consensus"):
if (a.motif not in consensuses): continue # (discard it)
elif (filterToKeep == "non consensus"):
if (a.motif in consensuses): continue # (discard it)
else: # if (filterToKeep == "no filter"):
pass
# copy the (unfiltered) alignment to the output
if (alignmentsWritten > 0): print
alignmentsWritten += 1
print "\n".join(a.lines)
# report the consensus, if we're supposed to
if (reportConsensus):
if (consensuses == []):
print "# consensus (none)"
else:
canonicalized = []
for motif in consensuses:
if (motif != a.motif) and (canonicalizeConsensuses):
(motif, strand) = canonical_motif(motif)
canonicalized += [motif]
print "# consensus %s" % ",".join(canonicalized)
# report the MSA from which the consensus was derived, if we're
# supposed to
if (reportMsa):
motifLen = len(a.motif)
positionLength = [1] * motifLen
for chunk in seqChunks:
for (motifIx, seqNucs) in enumerate(chunk):
if (seqNucs == None): continue
positionLength[motifIx] = max(positionLength[motifIx],
len(seqNucs))
line = []
for (motifIx, motifNuc) in enumerate(a.motif):
line += [motifNuc.ljust(positionLength[motifIx], ".")]
print "# msa.query %s" % "".join(line)
for chunk in seqChunks:
line = []
for (motifIx, seqNucs) in enumerate(chunk):
if (seqNucs == None):
line += ["." * positionLength[motifIx]]
elif (seqNucs == a.motif[motifIx]):
line += ["=" * positionLength[motifIx]]
else:
line += [seqNucs.ljust(positionLength[motifIx], ".")]
print "# msa.seq %s" % "".join(line)
if (requireEof):
print "# ncrf end-of-file"
