def parseCommandLineOptions(args, returnSignificantOffsets=True):
"""
Deal with the various command-line options added to the ArgumentParser
instance by addCommandLineOptions.
@param args: The result of calling C{parse_args} on an C{ArgumentParser}
instance (the one that was passed to C{addCommandLineOptions}, unless
we're testing).
@param returnSignificantOffsets: If C{True} also return a list of the
significant offsets (else that element of the return value will be
C{None}).
@return: A C{tuple}: (genomeLength, alignedReads, padddedSAM,
readCountAtOffset, baseCountAtOffset, readsAtOffset,
significantOffsets).
"""
genomeLength = None
alignedReads = []
samFilter = SAMFilter.parseFilteringOptions(args)
if samFilter.referenceIds and len(samFilter.referenceIds) > 1:
raise ValueError('Only one reference id can be given.')
referenceLengths = samFilter.referenceLengths()
if len(referenceLengths) == 1:
referenceId, genomeLength = referenceLengths.popitem()
else:
raise ValueError(
'If you do not specify a reference sequence with '
'--referenceId, the SAM/BAM file must contain exactly one '
'reference. But %s contains %d.' %
(args.samfile, len(referenceLengths)))
paddedSAM = PaddedSAM(samFilter)
for query in paddedSAM.queries():
alignedReads.append(AlignedRead(query.id, query.sequence))
readCountAtOffset, baseCountAtOffset, readsAtOffset = gatherData(
genomeLength, alignedReads)
if returnSignificantOffsets:
significantOffsets = list(
findSignificantOffsets(baseCountAtOffset, readCountAtOffset,
args.minReads, args.homogeneousCutoff))
for read in alignedReads:
read.setSignificantOffsets(significantOffsets)
else:
significantOffsets = None
return (genomeLength, alignedReads, paddedSAM, readCountAtOffset,
baseCountAtOffset, readsAtOffset, significantOffsets)
'that is provided by the SAMFilter.addFilteringOptions will be '
'silently ignored!'))
args = parser.parse_args()
if args.noOffsets and args.noStats:
print(
'You have used both --noOffsets and --noStats, so there is no '
'output!',
file=sys.stderr)
sys.exit(1)
# We don't have a file of reads, we just want a read filter that we can use
# to filter the SAM file query sequences and to get reference lengths from.
reads = parseFASTAFilteringCommandLineOptions(args, Reads())
samFilter = SAMFilter.parseFilteringOptions(args, reads.filterRead)
printOffsets = not args.noOffsets
printStats = not args.noStats
if samFilter.referenceIds and len(samFilter.referenceIds) > 1:
print(
'Only one reference id can be given. To calculate coverage for more '
'than one reference, run this script multiple times.',
file=sys.stderr)
sys.exit(1)
try:
referenceLengths = samFilter.referenceLengths()
except UnknownReference:
referenceId = samFilter.referenceIds.pop()
help='If given, write (gzip compressed) BAM output.')
parser.add_argument(
'--checkResultCount',
type=int,
help=('The number of alignments expected in the output. If this '
'number is not seen, the script exits with status 1 (and an '
'error message is also printed, unless --quiet was used).'))
addFASTAFilteringCommandLineOptions(parser)
SAMFilter.addFilteringOptions(parser)
args = parser.parse_args()
reads = parseFASTAFilteringCommandLineOptions(args, Reads())
samFilter = SAMFilter.parseFilteringOptions(args,
reads.filterRead,
storeQueryIds=True)
# The following 'if' has a False in it to make it always fail. That's
# because pysam issue 716 (see below) did not fix the problem as I had
# hoped. Instead it throws an error if you pass a header that has a
# modified SQ key with reference ids and there's a difference it
# doesn't like. It's always safe to use the 'else' below, with the
# slight downside being that its header will mention all sequence ids,
# even if you only want a lesser number (via --referenceId). I'm
# leaving the code here because this is how you would do it, and it
# might be possible to just copy the 'header' dict below and further
# adjust it to avoid the pysam error.
if False and samFilter.referenceIds:
# Make a header that only includes the wanted reference ids (if
# any).
'we cut the inserted bases out of the aligned query and save the '
'information about what would have been inserted and where. That '
'information is printed by this option. The output gives the '
'0-based offset where the inserted base would be placed, followed '
'by a list of the nucleotides that were suggested as being '
'inserted and the number of times each nucleotide was suggested. '
'So for example the output might contain "27: T:3, G:10" which '
'indicates that 13 query (3 with T and 10 with G) matches would '
'insert a nucleotide into the reference at offset 27.'))
SAMFilter.addFilteringOptions(parser)
addFASTAFilteringCommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTAFilteringCommandLineOptions(args, Reads())
samFilter = SAMFilter.parseFilteringOptions(
args, filterRead=reads.filterRead)
paddedSAM = PaddedSAM(samFilter)
for read in paddedSAM.queries(rcSuffix=args.rcSuffix, rcNeeded=args.rcNeeded):
print(read.toString('fasta'), end='')
if args.listReferenceInsertions:
if paddedSAM.referenceInsertions:
print('(0-based) insertions into the reference:\n%s' %
nucleotidesToStr(paddedSAM.referenceInsertions, ' '),
file=sys.stderr)
else:
print('No matches required an insertion into the reference.',
file=sys.stderr)
