def parseFASTAFilteringCommandLineOptions(args, reads):
"""
Examine parsed FASTA filtering command-line options and return filtered
reads.
@param args: An argparse namespace, as returned by the argparse
C{parse_args} function.
@param reads: A C{Reads} instance to filter.
@return: The filtered C{Reads} instance.
"""
keepSequences = (
parseRangeString(args.keepSequences, convertToZeroBased=True)
if args.keepSequences else None)
removeSequences = (
parseRangeString(args.removeSequences, convertToZeroBased=True)
if args.removeSequences else None)
return reads.filter(
minLength=args.minLength, maxLength=args.maxLength,
whitelist=set(args.whitelist) if args.whitelist else None,
blacklist=set(args.blacklist) if args.blacklist else None,
whitelistFile=args.whitelistFile, blacklistFile=args.blacklistFile,
titleRegex=args.titleRegex,
negativeTitleRegex=args.negativeTitleRegex,
keepSequences=keepSequences, removeSequences=removeSequences,
head=args.head, removeDuplicates=args.removeDuplicates,
removeDuplicatesById=args.removeDuplicatesById,
randomSubset=args.randomSubset, trueLength=args.trueLength,
sampleFraction=args.sampleFraction,
sequenceNumbersFile=args.sequenceNumbersFile)
def parseFASTAEditingCommandLineOptions(args, reads):
"""
Examine parsed FASTA editing command-line options and return information
about kept sites and sequences.
@param args: An argparse namespace, as returned by the argparse
C{parse_args} function.
@param reads: A C{Reads} instance to filter.
@return: The filtered C{Reads} instance.
"""
removeGaps = args.removeGaps
removeDescriptions = args.removeDescriptions
truncateTitlesAfter = args.truncateTitlesAfter
keepSites = (
parseRangeString(args.keepSites, convertToZeroBased=True)
if args.keepSites else None)
if args.keepSitesFile:
keepSites = keepSites or set()
with open(args.keepSitesFile) as fp:
for lineNumber, line in enumerate(fp):
try:
keepSites.update(
parseRangeString(line, convertToZeroBased=True))
except ValueError as e:
raise ValueError(
'Keep sites file %r line %d could not be parsed: '
'%s' % (args.keepSitesFile, lineNumber, e))
removeSites = (
parseRangeString(args.removeSites, convertToZeroBased=True)
if args.removeSites else None)
if args.removeSitesFile:
removeSites = removeSites or set()
with open(args.removeSitesFile) as fp:
for lineNumber, line in enumerate(fp):
try:
removeSites.update(
parseRangeString(line, convertToZeroBased=True))
except ValueError as e:
raise ValueError(
'Remove sites file %r line %d parse error: %s'
% (args.removeSitesFile, lineNumber, e))
return reads.filter(
removeGaps=removeGaps,
truncateTitlesAfter=truncateTitlesAfter,
removeDescriptions=removeDescriptions,
idLambda=args.idLambda, readLambda=args.readLambda,
keepSites=keepSites, removeSites=removeSites,
reverse=args.reverse, reverseComplement=args.reverseComplement)
def parseFASTAEditingCommandLineOptions(args, reads):
"""
Examine parsed FASTA editing command-line options and return information
about kept sites and sequences.
@param args: An argparse namespace, as returned by the argparse
C{parse_args} function.
@param reads: A C{Reads} instance to filter.
@return: The filtered C{Reads} instance.
"""
removeGaps = args.removeGaps
removeDescriptions = args.removeDescriptions
truncateTitlesAfter = args.truncateTitlesAfter
keepSites = (parseRangeString(args.keepSites, convertToZeroBased=True)
if args.keepSites else None)
if args.keepSitesFile:
keepSites = keepSites or set()
with open(args.keepSitesFile) as fp:
for lineNumber, line in enumerate(fp):
try:
keepSites.update(
parseRangeString(line, convertToZeroBased=True))
except ValueError as e:
raise ValueError(
'Keep sites file %r line %d could not be parsed: '
'%s' % (args.keepSitesFile, lineNumber, e))
removeSites = (parseRangeString(args.removeSites, convertToZeroBased=True)
if args.removeSites else None)
if args.removeSitesFile:
removeSites = removeSites or set()
with open(args.removeSitesFile) as fp:
for lineNumber, line in enumerate(fp):
try:
removeSites.update(
parseRangeString(line, convertToZeroBased=True))
except ValueError as e:
raise ValueError(
'Remove sites file %r line %d parse error: %s' %
(args.removeSitesFile, lineNumber, e))
return reads.filter(removeGaps=removeGaps,
truncateTitlesAfter=truncateTitlesAfter,
removeDescriptions=removeDescriptions,
idLambda=args.idLambda,
readLambda=args.readLambda,
keepSites=keepSites,
removeSites=removeSites,
reverse=args.reverse,
reverseComplement=args.reverseComplement)
def testZeroConversion(self):
"""
If we ask for zero conversion, the result must be as expected.
"""
self.assertEqual({3, 5, 6, 7, 8, 9, 10, 11},
parseRangeString('6-8,9,10-12,4',
convertToZeroBased=True))
def testZeroConversion(self):
"""
If we ask for zero conversion, the result must be as expected.
"""
self.assertEqual({3, 5, 6, 7, 8, 9, 10, 11},
parseRangeString('6-8,9,10-12,4',
convertToZeroBased=True))
def parseFASTAFilteringCommandLineOptions(args, reads):
"""
Examine parsed FASTA filtering command-line options and return filtered
reads.
@param args: An argparse namespace, as returned by the argparse
C{parse_args} function.
@param reads: A C{Reads} instance to filter.
@return: The filtered C{Reads} instance.
"""
keepSequences = (parseRangeString(args.keepSequences,
convertToZeroBased=True)
if args.keepSequences else None)
removeSequences = (parseRangeString(args.removeSequences,
convertToZeroBased=True)
if args.removeSequences else None)
return reads.filter(
minLength=args.minLength,
maxLength=args.maxLength,
whitelist=set(args.whitelist) if args.whitelist else None,
blacklist=set(args.blacklist) if args.blacklist else None,
whitelistFile=args.whitelistFile,
blacklistFile=args.blacklistFile,
titleRegex=args.titleRegex,
negativeTitleRegex=args.negativeTitleRegex,
keepSequences=keepSequences,
removeSequences=removeSequences,
head=args.head,
removeDuplicates=args.removeDuplicates,
removeDuplicatesById=args.removeDuplicatesById,
randomSubset=args.randomSubset,
trueLength=args.trueLength,
sampleFraction=args.sampleFraction,
sequenceNumbersFile=args.sequenceNumbersFile)
def testSingleRange(self):
"""
A single range must result in the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6-10'))
def testSingleNumberSpaceBeforeAndAfter(self):
"""
A single number preceeded and followed by whitespace must result in
the expected set.
"""
self.assertEqual({6}, parseRangeString(' 6 '))
def testSingleNumber(self):
"""
A single number must result in the expected set.
"""
self.assertEqual({6}, parseRangeString('6'))
if args.align:
len1, len2 = map(len, reads)
if len1 == len2:
print('Pre-alignment, sequence lengths were identical: %s' % len1)
else:
print('Pre-alignment, sequence lengths: %d, %d (difference %d)' %
(len1, len2, abs(len1 - len2)))
# Align.
reads = needle(reads)
if args.alignmentFile:
assert reads.save(args.alignmentFile) == 2
offsets = (parseRangeString(args.sites, convertToZeroBased=True)
if args.sites else None)
read1, read2 = reads
len1, len2 = map(len, reads)
identicalLengths = len1 == len2
# Sanity check.
if args.align:
assert identicalLengths
match = compareDNAReads(read1,
read2,
matchAmbiguous=(not args.strict),
offsets=offsets)
def testTwoRangesAndTwoNumbers(self):
"""
Two ranges and two numbers must result in the expected set.
"""
self.assertEqual({4, 6, 7, 8, 9, 10, 11, 12},
parseRangeString('6-8,9,10-12,4'))
def testTwoOverlappingRanges(self):
"""
Two overlapping ranges must result in the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6-9,7-10'))
def testTwoOverlappingRanges(self):
"""
Two overlapping ranges must result in the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6-9,7-10'))
def testTwoRanges(self):
"""
Two ranges must result in the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6-8,9-10'))
def testSingleRangeWithSpaceBeforeAfterHyphen(self):
"""
A single range with spaces before and after the hyphen must result in
the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6 - 10'))
def testSingleRange(self):
"""
A single range must result in the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6-10'))
def testSingleNumberSpaceBeforeAndAfter(self):
"""
A single number preceeded and followed by whitespace must result in
the expected set.
"""
self.assertEqual({6}, parseRangeString(' 6 '))
def testSingleNumber(self):
"""
A single number must result in the expected set.
"""
self.assertEqual({6}, parseRangeString('6'))
def testSingleRangeWithSpaceBeforeAfterHyphen(self):
"""
A single range with spaces before and after the hyphen must result in
the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6 - 10'))
def testTwoRanges(self):
"""
Two ranges must result in the expected set.
"""
self.assertEqual({6, 7, 8, 9, 10}, parseRangeString('6-8,9-10'))
def parseFASTAFilteringCommandLineOptions(args, reads):
"""
Examine parsed command-line options and return information about kept
sites and sequences.
@param args: An argparse namespace, as returned by the argparse
C{parse_args} function.
@param reads: A C{Reads} instance to filter.
@return: The filtered C{Reads} instance.
"""
keepSequences = (
parseRangeString(args.keepSequences, convertToZeroBased=True)
if args.keepSequences else None)
removeSequences = (
parseRangeString(args.removeSequences, convertToZeroBased=True)
if args.removeSequences else None)
keepSites = (
parseRangeString(args.keepSites, convertToZeroBased=True)
if args.keepSites else None)
if args.keepSitesFile:
keepSites = keepSites or set()
with open(args.keepSitesFile) as fp:
for lineNumber, line in enumerate(fp):
try:
keepSites.update(
parseRangeString(line, convertToZeroBased=True))
except ValueError as e:
raise ValueError(
'Keep sites file %r line %d could not be parsed: %s'
% (args.keepSitesFile, lineNumber, e))
removeSites = (
parseRangeString(args.removeSites, convertToZeroBased=True)
if args.removeSites else None)
if args.removeSitesFile:
removeSites = removeSites or set()
with open(args.removeSitesFile) as fp:
for lineNumber, line in enumerate(fp):
try:
removeSites.update(
parseRangeString(line, convertToZeroBased=True))
except ValueError as e:
raise ValueError(
'Remove sites file %r line %d parse error: %s'
% (args.removeSitesFile, lineNumber, e))
return reads.filter(
minLength=args.minLength, maxLength=args.maxLength,
removeGaps=args.removeGaps,
whitelist=set(args.whitelist) if args.whitelist else None,
blacklist=set(args.blacklist) if args.blacklist else None,
whitelistFile=args.whitelistFile, blacklistFile=args.blacklistFile,
titleRegex=args.titleRegex,
negativeTitleRegex=args.negativeTitleRegex,
truncateTitlesAfter=args.truncateTitlesAfter,
keepSequences=keepSequences, removeSequences=removeSequences,
head=args.head, removeDuplicates=args.removeDuplicates,
removeDuplicatesById=args.removeDuplicatesById,
removeDescriptions=args.removeDescriptions,
randomSubset=args.randomSubset, trueLength=args.trueLength,
sampleFraction=args.sampleFraction,
sequenceNumbersFile=args.sequenceNumbersFile,
idLambda=args.idLambda, readLambda=args.readLambda,
keepSites=keepSites, removeSites=removeSites)
def testTwoRangesAndANumber(self):
"""
Two ranges and a number must result in the expected set.
"""
self.assertEqual({6, 7, 8, 10}, parseRangeString('6-8,10'))
def testTwoRangesAndTwoNumbers(self):
"""
Two ranges and two numbers must result in the expected set.
"""
self.assertEqual({4, 6, 7, 8, 9, 10, 11, 12},
parseRangeString('6-8,9,10-12,4'))
def testTwoRangesAndANumber(self):
"""
Two ranges and a number must result in the expected set.
"""
self.assertEqual({6, 7, 8, 10}, parseRangeString('6-8,10'))
if args.align:
len1, len2 = map(len, reads)
if len1 == len2:
print('Pre-alignment, sequence lengths were identical: %s' % len1)
else:
print('Pre-alignment, sequence lengths: %d, %d (difference %d)' % (
len1, len2, abs(len1 - len2)))
# Align.
reads = needle(reads)
if args.alignmentFile:
assert reads.save(args.alignmentFile) == 2
offsets = (parseRangeString(args.sites, convertToZeroBased=True)
if args.sites else None)
read1, read2 = reads
len1, len2 = map(len, reads)
identicalLengths = len1 == len2
# Sanity check.
if args.align:
assert identicalLengths
match = compareDNAReads(read1, read2, matchAmbiguous=(not args.strict),
offsets=offsets)
x = 'Post-alignment, sequence' if args.align else 'Sequence'
if identicalLengths: