def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv: argv = sys.argv
# setup command line parser
parser = E.OptionParser( version = "%prog version: $Id: script_template.py 2871 2010-03-03 10:20:44Z andreas $",
usage = globals()["__doc__"] )
parser.add_option("-a", "--fastq1", dest="fastq1", type="string",
help="supply read1 fastq file" )
parser.add_option("-b", "--fastq2", dest="fastq2", type="string",
help="supply read2 fastq file" )
## add common options (-h/--help, ...) and parse command line
(options, args) = E.Start( parser, argv = argv )
fastq1 = IOTools.openFile(options.fastq1)
fastq2 = IOTools.openFile(options.fastq2)
E.info("iterating over fastq files")
f1_count = 0
for f1, f2 in itertools.izip_longest(Fastq.iterate(fastq1), Fastq.iterate(fastq2)):
if not (f1 and f2) or (not f2 and f1):
try:
raise PairedReadError("unpaired reads detected. Are files sorted? are files of equal length?")
except PairedReadError, e:
raise PairedReadError(e), None, sys.exc_info()[2]
else:
assert f1.identifier.endswith("/1") and f2.identifier.endswith("/2"), "Reads in file 1 must end with /1 and reads in file 2 with /2"
options.stdout.write(">%s\n%s\n>%s\n%s\n" % (f1.identifier, f1.seq, f2.identifier, f2.seq))
f1_count += 1
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-a",
"--first-fastq-file",
dest="fastq1",
type="string",
help="supply read1 fastq file")
parser.add_option("-b",
"--second-fastq-file",
dest="fastq2",
type="string",
help="supply read2 fastq file")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv)
if args and len(args) == 2:
options.fastq1, options.fastq2 = args
fastq1 = IOTools.open_file(options.fastq1)
fastq2 = IOTools.open_file(options.fastq2)
E.info("iterating over fastq files")
f1_count = 0
for f1, f2 in zip_longest(Fastq.iterate(fastq1), Fastq.iterate(fastq2)):
if not (f1 and f2) or (not f2 and f1):
try:
raise PairedReadError(
"unpaired reads detected. Are files sorted? are "
"files of equal length?")
except PairedReadError as e:
raise PairedReadError(e).with_traceback(sys.exc_info()[2])
else:
assert f1.identifier.endswith("/1") and \
f2.identifier.endswith("/2"), \
"Reads in file 1 must end with /1 and reads in file 2 with /2"
options.stdout.write(
">%s\n%s\n>%s\n%s\n" %
(f1.identifier, f1.seq, f2.identifier, f2.seq))
f1_count += 1
E.info("output: %i pairs" % f1_count)
# write footer and output benchmark information.
E.stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(
version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option(
"-a", "--first-fastq-file", dest="fastq1", type="string",
help="supply read1 fastq file")
parser.add_option(
"-b", "--second-fastq-file", dest="fastq2", type="string",
help="supply read2 fastq file")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if args and len(args) == 2:
options.fastq1, options.fastq2 = args
fastq1 = IOTools.openFile(options.fastq1)
fastq2 = IOTools.openFile(options.fastq2)
E.info("iterating over fastq files")
f1_count = 0
for f1, f2 in zip_longest(Fastq.iterate(fastq1),
Fastq.iterate(fastq2)):
if not (f1 and f2) or (not f2 and f1):
try:
raise PairedReadError(
"unpaired reads detected. Are files sorted? are "
"files of equal length?")
except PairedReadError as e:
raise PairedReadError(e).with_traceback(sys.exc_info()[2])
else:
assert f1.identifier.endswith("/1") and \
f2.identifier.endswith("/2"), \
"Reads in file 1 must end with /1 and reads in file 2 with /2"
options.stdout.write(
">%s\n%s\n>%s\n%s\n" %
(f1.identifier, f1.seq, f2.identifier, f2.seq))
f1_count += 1
E.info("output: %i pairs" % f1_count)
# write footer and output benchmark information.
E.Stop()
def filterReadsByPrimerMatch(infile, outfiles):
'''Filter out reads where the start of read 1 does not match primer sequence (14bp)'''
to_cluster = True
primer = "a"
if infile.find("_b.") > 0:
primer = "b"
if primer == "a":
primer_seq = PARAMS["grep_primer_a"]
else:
primer_seq = PARAMS["grep_primer_b"]
grep_filter_length = PARAMS["grep_filter_length"]
primer_subseq = primer_seq[:grep_filter_length]
track = P.snip(os.path.basename(infile), ".fastq.1.gz")
infile2 = track + ".fastq.2.gz"
outfile1, outfile2 = outfiles
tempfile = "filtered/" + track + ".filtered.fastq.1.gz"
# filter by primer match
fastq_in = open(infile, "r")
fastq_out = open(tempfile, "wb")
for read in fq.iterate(fastq_in):
if read.seq[:grep_filter_length] == primer_subseq:
fastq_out.writeln("@" + read.id)
fastq_out.writeln(read.seq)
fastq_out.writeln("+")
fastq_out.writeln(read.qual)
fastq_in.close()
fastq_out.close()
# reconcile read pairs
statement = '''python %(scriptsdir)s/fastqs2fastq.py --method=reconcile %(tempfile)s %(infile2)s --output-pattern=filtered/%(track)s.reconciled.fastq.%%i.gz'''
P.run()
def buildTrueTaxonomicRelativeAbundances(infiles, outfile):
'''
get species level relative abundances for the simulateds
data. This involes creating maps between different identifiers
from the NCBI taxonomy. This is so that the results are comparable
to species level analysis from metaphlan
'''
levels = ["species", "genus", "family", "order", "class", "phylum"]
taxa = open(infiles[1])
header = taxa.readline()
gi2taxa = collections.defaultdict(list)
for line in taxa.readlines():
data = line[:-1].split("\t")
gi, strain, species, genus, family, order, _class, phylum = data[
0], data[1], data[2], data[3], data[4], data[5], data[6], data[7]
gi2taxa[gi] = (species, genus, family, order, _class, phylum)
outf = open(outfile, "w")
outf.write("level\ttaxa\trelab\n")
for i in range(len(levels)):
total = 0
result = collections.defaultdict(int)
for fastq in Fastq.iterate(IOTools.openFile(infiles[0])):
total += 1
gi = fastq.identifier.split("|")[1]
result[gi2taxa[gi][i]] += 1
for taxa, value in result.iteritems():
outf.write("%s\t%s\t%s\n" %
(levels[i], taxa, float(value) / total))
outf.close()
def filterReadsByPrimerMatch(infile, outfiles):
'''Filter out reads where the start of read 1 does not match primer sequence (14bp)'''
to_cluster = True
primer = "a"
if infile.find("_b.") > 0:
primer = "b"
if primer == "a":
primer_seq = PARAMS["grep_primer_a"]
else:
primer_seq = PARAMS["grep_primer_b"]
grep_filter_length = PARAMS["grep_filter_length"]
primer_subseq = primer_seq[:grep_filter_length]
track = P.snip(os.path.basename(infile), ".fastq.1.gz")
infile2 = track + ".fastq.2.gz"
outfile1, outfile2 = outfiles
tempfile = "filtered/" + track + ".filtered.fastq.1.gz"
# filter by primer match
fastq_in = open(infile, "r")
fastq_out = open(tempfile, "wb")
for read in fq.iterate(fastq_in):
if read.seq[:grep_filter_length] == primer_subseq:
fastq_out.writeln("@" + read.id)
fastq_out.writeln(read.seq)
fastq_out.writeln("+")
fastq_out.writeln(read.qual)
fastq_in.close()
fastq_out.close()
# reconcile read pairs
statement = '''python %(scriptsdir)s/fastqs2fastq.py --method=reconcile %(tempfile)s %(infile2)s --output-filename-pattern=filtered/%(track)s.reconciled.fastq.%%i.gz'''
P.run()
def buildTrueTaxonomicRelativeAbundances(infiles, outfile):
'''
get species level relative abundances for the simulateds
data. This involes creating maps between different identifiers
from the NCBI taxonomy. This is so that the results are comparable
to species level analysis from metaphlan
'''
levels = ["species", "genus", "family", "order", "class", "phylum"]
taxa = open(infiles[1])
header = taxa.readline()
gi2taxa = collections.defaultdict(list)
for line in taxa.readlines():
data = line[:-1].split("\t")
gi, strain, species, genus, family, order, _class, phylum = data[
0], data[1], data[2], data[3], data[4], data[5], data[6], data[7]
gi2taxa[gi] = (species, genus, family, order, _class, phylum)
outf = open(outfile, "w")
outf.write("level\ttaxa\trelab\n")
for i in range(len(levels)):
total = 0
result = collections.defaultdict(int)
for fastq in Fastq.iterate(IOTools.openFile(infiles[0])):
total += 1
gi = fastq.identifier.split("|")[1]
result[gi2taxa[gi][i]] += 1
for taxa, value in result.iteritems():
outf.write("%s\t%s\t%s\n" %
(levels[i], taxa, float(value) / total))
outf.close()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id: cgat_script_template.py 2871 2010-03-03 10:20:44Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-f", "--change-format", dest="change_format", type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer'),
help="guess quality score format and set quality scores to format [default=%default].")
parser.add_option("--guess-format", dest="guess_format", type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer'),
help="quality score format to assume if ambiguous [default=%default].")
parser.add_option("--pattern", dest="pattern", type="string",
help="filename prefix [default=%default].")
parser.set_defaults(
change_format=None,
guess_format=None,
pattern="%s.gz"
)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
c = E.Counter()
outfile_seq = IOTools.openFile(options.pattern % "csfasta", "w")
outfile_qual = IOTools.openFile(options.pattern % "qual", "w")
if options.change_format:
iter = Fastq.iterate_convert(options.stdin,
format=options.change_format,
guess=options.guess_format)
else:
iter = Fastq.iterate(options.stdin)
for record in iter:
c.input += 1
outfile_seq.write(">%s\n%s\n" % (record.identifier, record.seq))
outfile_qual.write(">%s\n%s\n" % (record.identifier, record.quals))
c.output += 1
outfile_seq.close()
outfile_qual.close()
# write footer and output benchmark information.
E.info("%s" % str(c))
E.Stop()
def replace(fastqfile, baseToReplace):
'''replaces the specified base with N'''
# use gzip as default to open the fastq file
outf = gzip.open("replaced_" + fastqfile, "w")
fastq = gzip.open(fastqfile)
iterator = Fastq.iterate(fastq)
for record in iterator:
x = list(record.seq)
x[int(baseToReplace)] = "N"
record.seq = "".join(x)
outf.write("@" + record.identifier + "\n" + record.seq + "\n" + "+" + record.identifier + "\n" + record.quals + "\n")
def replace(fastqfile, baseToReplace):
'''replaces the specified base with N'''
# use gzip as default to open the fastq file
outf = gzip.open("replaced_" + fastqfile, "w")
fastq = gzip.open(fastqfile)
iterator = Fastq.iterate(fastq)
for record in iterator:
x = list(record.seq)
x[int(baseToReplace)] = "N"
record.seq = "".join(x)
outf.write("@" + record.identifier + "\n" + record.seq + "\n" + "+" +
record.identifier + "\n" + record.quals + "\n")
def buildExpectedCoverageOverGenomes(infiles, outfile):
'''
take sequence files and estimate the theoretical
coverage we would get over genomes in the
sample i.e. at 1X coverage
'''
# if paired end then will have to multiply
# by two
multiply = False
if infiles[0].endswith(".fastq.1.gz"):
multiply = True
# the theoretical coverage is defined as
# (read length (L) * no. reads (N)) / genome size (G) (bp)
# get genome sizes into memory
genomes = open(infiles[1])
header = genomes.readline()
genome_sizes = {}
for line in genomes.readlines():
data = line[:-1].split("\t")
gi = data[0].split("_")[1]
size = data[1]
genome_sizes[gi] = size
# get the expected genome size
expected_genome_sizes = collections.defaultdict(int)
E.info("iterating over fastq file")
for fastq in Fastq.iterate(IOTools.openFile(infiles[0])):
gi = fastq.identifier.split("|")[1]
expected_genome_sizes[gi] += 1
E.info("iterating over fastq file: DONE")
# get the proportion of each genome covered
outf = open(outfile, "w")
outf.write("gi\texpected_coverage\n")
for gi, size in expected_genome_sizes.iteritems():
if multiply:
size = size * 2
if gi not in genome_sizes:
E.warn("could not find gi no. %s in dictionary" % gi)
continue
proportion_coverage = float(size) / float(genome_sizes[gi])
if proportion_coverage > 1:
proportion_coverage = 1
outf.write("%s\t%f\n" % (gi, proportion_coverage))
outf.close()
def buildExpectedCoverageOverGenomes(infiles, outfile):
'''
take sequence files and estimate the theoretical
coverage we would get over genomes in the
sample i.e. at 1X coverage
'''
# if paired end then will have to multiply
# by two
multiply = False
if infiles[0].endswith(".fastq.1.gz"):
multiply = True
# the theoretical coverage is defined as
# (read length (L) * no. reads (N)) / genome size (G) (bp)
# get genome sizes into memory
genomes = open(infiles[1])
header = genomes.readline()
genome_sizes = {}
for line in genomes.readlines():
data = line[:-1].split("\t")
gi = data[0].split("_")[1]
size = data[1]
genome_sizes[gi] = size
# get the expected genome size
expected_genome_sizes = collections.defaultdict(int)
E.info("iterating over fastq file")
for fastq in Fastq.iterate(IOTools.openFile(infiles[0])):
gi = fastq.identifier.split("|")[1]
expected_genome_sizes[gi] += 1
E.info("iterating over fastq file: DONE")
# get the proportion of each genome covered
outf = open(outfile, "w")
outf.write("gi\texpected_coverage\n")
for gi, size in expected_genome_sizes.iteritems():
if multiply:
size = size * 2
if gi not in genome_sizes:
E.warn("could not find gi no. %s in dictionary" % gi)
continue
proportion_coverage = float(size) / float(genome_sizes[gi])
if proportion_coverage > 1:
proportion_coverage = 1
outf.write("%s\t%f\n" % (gi, proportion_coverage))
outf.close()
def preprocessIdba(infile, outfile):
'''
preprocess pooled reads for IDBA
'''
# check for second read in the pair
if infile.endswith(".fastq.gz"):
E.info("converting fastq file to fasta file")
outf = open(outfile, "w")
for fastq in Fastq.iterate(IOTools.openFile(infile)):
outf.write("%s\n%s\n" % (">" + fastq.identifier, fastq.seq))
outf.close()
elif infile.endswith(".1.gz"):
read2 = P.snip(infile, ".1.gz") + ".2.gz"
assert os.path.exists(read2), "file does not exist %s" % read2
statement = '''python %(scriptsdir)s/fastqs2fasta.py
-a %(infile)s
-b %(read2)s
--log=%(infile)s.log
> %(outfile)s'''
P.run()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv: argv = sys.argv
# setup command line parser
parser = E.OptionParser(
version=
"%prog version: $Id: cgat_script_template.py 2871 2010-03-03 10:20:44Z andreas $",
usage=globals()["__doc__"])
parser.add_option(
"-f",
"--change-format",
dest="change_format",
type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer'),
help=
"guess quality score format and set quality scores to format [default=%default]."
)
parser.add_option(
"--guess-format",
dest="guess_format",
type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer'),
help="quality score format to assume if ambiguous [default=%default].")
parser.add_option("--sample",
dest="sample",
type="float",
help="sample a proportion of reads [default=%default].")
parser.add_option("--pair",
dest="pair",
type="string",
help="if data is paired, filename with second pair. "
"Implemented for sampling [default=%default].")
parser.add_option("--outfile-pair",
dest="outfile_pair",
type="string",
help="if data is paired, filename for second pair. "
"Implemented for sampling [default=%default].")
parser.add_option(
"--uniq",
dest="uniq",
action="store_true",
help="remove duplicate reads (by name) [default=%default].")
parser.add_option(
"--apply",
dest="apply",
type="string",
help=
"apply a filter to fastq file (taking only reads in filename) [default=%default]."
)
parser.add_option("--trim3",
dest="trim3",
type="int",
help="trim # bases from 3' end [default=%default].")
parser.add_option("--sort",
dest="sort",
action="store_true",
help="sort fastq by sequence id [default=%default].")
parser.add_option(
"--seed",
dest="seed",
type="int",
help="seed for random number generator [default=%default].")
parser.add_option(
"--renumber-ids",
dest="renumber_ids",
type="string",
help="rename reads in file by pattern [default=%default]")
parser.set_defaults(change_format=None,
guess_format=None,
sample=None,
trim3=None,
pair=None,
apply=None,
uniq=False,
outfile_pair=None,
sort=None,
seed=None,
renumber_ids=None)
## add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
c = E.Counter()
if options.change_format:
for record in Fastq.iterate_convert(options.stdin,
format=options.change_format,
guess=options.guess_format):
c.input += 1
options.stdout.write("%s\n" % record)
c.output += 1
elif options.sample:
sample_threshold = min(1.0, options.sample)
random.seed(options.seed)
if options.pair:
if not options.outfile_pair:
raise ValueError(
"please specify output filename for second pair (--outfile-pair)"
)
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.outfile_pair, "w")
for record1, record2 in itertools.izip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.openFile(options.pair))):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
outfile1.write("%s\n" % record1)
outfile2.write("%s\n" % record2)
for record in Fastq.iterate(options.stdin):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.apply:
ids = set(IOTools.readList(IOTools.openFile(options.apply)))
for record in Fastq.iterate(options.stdin):
c.input += 1
if re.sub(" .*", "", record.identifier).strip() in ids:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.trim3:
trim3 = options.trim3
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim(trim3)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.uniq:
keys = set()
for record in Fastq.iterate(options.stdin):
c.input += 1
if record.identifier in keys: continue
else: keys.add(record.identifier)
options.stdout.write("%s\n" % record)
c.output += 1
# Need to change this to incorporate both pairs
elif options.sort:
if not options.pair:
# This is quicker for a single fastq file
statement = "paste - - - - | sort -k1,1 -t ' ' | tr '\t' '\n'"
os.system(statement)
else:
if not options.outfile_pair:
raise ValueError(
"please specify output filename for second pair (--outfile-pair)"
)
E.warn(
"consider sorting individual fastq files - this is memory intensive"
)
entries1 = {}
entries2 = {}
for record1, record2 in itertools.izip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.openFile(options.pair))):
entries1[record1.identifier[:-2]] = (record1.seq,
record1.quals)
entries2[record2.identifier[:-2]] = (record2.seq,
record2.quals)
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.outfile_pair, "w")
assert len(
set(entries1.keys()).intersection(set(entries2.keys()))
) == len(entries1), """paired files do not contain the same reads
need to reconcile files"""
for entry in sorted(entries1):
outfile1.write("@%s/1\n%s\n+\n%s\n" %
(entry, entries1[entry][0], entries1[entry][1]))
outfile2.write("@%s/2\n%s\n+\n%s\n" %
(entry, entries2[entry][0], entries2[entry][1]))
elif options.renumber_ids:
id_count = 1
for record in Fastq.iterate(options.stdin):
record.identifier = options.renumber_ids % id_count
id_count += 1
options.stdout.write("@%s\n%s\n+\n%s\n" %
(record.identifier, record.seq, record.quals))
## write footer and output benchmark information.
E.info("%s" % str(c))
E.Stop()
def process_cgat(options):
c = E.Counter()
assert options.input_fastq_file == "-"
if options.method == "change-format":
for record in Fastq.iterate_convert(options.stdin,
format=options.target_format,
guess=options.guess_format):
c.input += 1
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "grep":
for record in Fastq.iterate(options.stdin):
if re.match(options.grep_pattern, record.seq):
options.stdout.write("%s\n" % record)
elif options.method == "reverse-complement":
for record in Fastq.iterate(options.stdin):
record.seq = Genomics.complement(record.seq)
record.quals = record.quals[::-1]
options.stdout.write("%s\n" % record)
elif options.method == "sample":
sample_threshold = min(1.0, options.sample_size)
random.seed(options.seed)
if options.pair:
if not options.output_filename_pattern:
raise ValueError("please specify output filename pattern for "
"second pair (--output-filename-pattern)")
outfile1 = options.stdout
outfile2 = IOTools.open_file(options.output_filename_pattern, "w")
for record1, record2 in zip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.open_file(options.pair))):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
outfile1.write("%s\n" % record1)
outfile2.write("%s\n" % record2)
else:
for record in Fastq.iterate(options.stdin):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.method == "apply":
ids = set(IOTools.read_list(IOTools.open_file(options.apply)))
for record in Fastq.iterate(options.stdin):
c.input += 1
if re.sub(" .*", "", record.identifier).strip() in ids:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.method == "trim3":
trim3 = options.nbases
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim(trim3)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "trim5":
trim5 = options.nbases
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim5(trim5)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "unique":
keys = set()
for record in Fastq.iterate(options.stdin):
c.input += 1
if record.identifier in keys:
continue
else:
keys.add(record.identifier)
options.stdout.write("%s\n" % record)
c.output += 1
# Need to change this to incorporate both pairs
elif options.method == "sort":
if not options.pair:
# This is quicker for a single fastq file
statement = "paste - - - - | sort -k1,1 -t ' ' | tr '\t' '\n'"
os.system(statement)
else:
if not options.output_filename_pattern:
raise ValueError(
"please specify output filename for second pair "
"(--output-filename-pattern)")
E.warn("consider sorting individual fastq files - "
"this is memory intensive")
entries1 = {}
entries2 = {}
for record1, record2 in zip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.open_file(options.pair))):
entries1[record1.identifier[:-2]] = (record1.seq,
record1.quals)
entries2[record2.identifier[:-2]] = (record2.seq,
record2.quals)
outfile1 = options.stdout
outfile2 = IOTools.open_file(options.output_filename_pattern, "w")
assert len(set(entries1.keys()).intersection(
set(entries2.keys()))) == len(entries1),\
"paired files do not contain the same reads "\
"need to reconcile files"
for entry in sorted(entries1):
outfile1.write("@%s/1\n%s\n+\n%s\n" %
(entry, entries1[entry][0], entries1[entry][1]))
outfile2.write("@%s/2\n%s\n+\n%s\n" %
(entry, entries2[entry][0], entries2[entry][1]))
elif options.method == "renumber-reads":
id_count = 1
for record in Fastq.iterate(options.stdin):
record.identifier = options.renumber_pattern % id_count
id_count += 1
options.stdout.write("@%s\n%s\n+\n%s\n" %
(record.identifier, record.seq, record.quals))
return c
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-b",
"--bamfile",
dest="bamfile",
type="string",
help="input bamfile to filter reads from")
parser.add_option("-r",
"--reads",
dest="reads",
type="choice",
choices=("mapped", "unmapped"),
help="type of read to keep")
parser.add_option("-s",
"--scriptsdir",
dest="scriptsdir",
type="string",
help="CGAT scripts directory")
parser.add_option("-i",
"--invert",
dest="invert",
action="store_true",
help="invert selection - if for example unmapped reads \
aren't output")
parser.set_defaults(bamfile=None,
reads="mapped",
scriptsdir="/ifs/devel/nicki/cgat_git/cgat/scripts",
invert=False)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
c = E.Counter()
c.input_alignments = 0
c.input_reads = 0
c.output_reads = 0
# output text file for reads TO KEEP
bam = pysam.Samfile(options.bamfile, "rb")
temp = P.getTempFile(".")
E.info("iterating over bam file")
for alignment in bam.fetch(until_eof=True):
c.input_alignments += 1
if options.reads == "unmapped":
if alignment.is_unmapped:
#c.input_alignments += 1
temp.write(alignment.qname + "\n")
elif options.reads == "mapped":
if not alignment.is_unmapped:
#c.input_alignments += 1
temp.write(alignment.qname + "\n")
temp.close()
tempname = temp.name
E.info("filtering fastq file")
# filter fastq file
ids = set(IOTools.readList(IOTools.openFile(tempname).readlines()))
c.input_alignments = len(ids)
for fastq in Fastq.iterate(options.stdin):
c.input_reads += 1
if (fastq.identifier.endswith("/1") or fastq.identifier.endswith("/2")
) and " " not in fastq.identifier:
identifier = fastq.identifier[:-2]
elif len(fastq.identifier.split(" ")) == 2:
identifier = fastq.identifier.split(" ")[0]
else:
identifier = fastq.identifier
if not options.invert:
if identifier in ids:
c.output_reads += 1
options.stdout.write("%s\n" % fastq)
else:
if identifier in ids: continue
c.output_reads += 1
options.stdout.write("%s\n" % fastq)
E.info(c)
os.unlink(tempname)
# write footer and output benchmark information.
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-m",
"--method",
dest="method",
type="choice",
choices=('join', ),
help="method to apply [default=%default].")
parser.set_defaults(method="join", )
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if len(args) != 2:
raise ValueError(
"please supply at least two fastq files on the commandline")
fn1, fn2 = args
c = E.Counter()
outfile = options.stdout
if options.method == "join":
# merge based on diagonals in dotplot
iter1 = Fastq.iterate(IOTools.openFile(fn1))
iter2 = Fastq.iterate(IOTools.openFile(fn2))
tuple_size = 2
for left, right in zip(iter1, iter2):
c.input += 1
# build dictionary of tuples
s1, q1 = left.seq, left.quals
d = collections.defaultdict(list)
for x in range(len(s1) - tuple_size):
d[s1[x:x + tuple_size]].append(x)
s2, q2 = right.seq, right.quals
# reverse complement
s2 = Genomics.complement(s2)
q2 = q2[::-1]
# compute list of offsets/diagonals
offsets = collections.defaultdict(int)
for x in range(len(s2) - tuple_size):
c = s2[x:x + tuple_size]
for y in d[c]:
offsets[x - y] += 1
# find maximum diagonal
sorted = sorted([(y, x) for x, y in offsets.items()])
max_count, max_offset = sorted[-1]
E.debug('%s: maximum offset at %i' % (left.identifier, max_offset))
# simple merge sequence
take = len(s2) - max_offset
merged_seq = s1 + s2[take:]
# simple merge quality scores
merged_quals = q1 + q2[take:]
new_entry = copy.copy(left)
new_entry.seq = merged_seq
new_entry.quals = merged_quals
outfile.write(new_entry)
c.output += 1
# write footer and output benchmark information.
E.info("%s" % str(c))
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id",
usage=globals()["__doc__"])
parser.add_option("-f",
"--target-format",
dest="change_format",
type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer'),
help="set quality scores to format "
"[default=%default].")
parser.add_option(
"--guess-format",
dest="guess_format",
type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer'),
help="quality score format to assume if ambiguous [default=%default].")
parser.add_option("--pattern-identifier",
dest="pattern",
type="string",
help="filename prefix [default=%default].")
parser.set_defaults(change_format=None, guess_format=None, pattern="%s.gz")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv)
c = E.Counter()
outfile_seq = IOTools.open_file(options.pattern % "csfasta", "w")
outfile_qual = IOTools.open_file(options.pattern % "qual", "w")
if options.change_format:
iter = Fastq.iterate_convert(options.stdin,
format=options.change_format,
guess=options.guess_format)
else:
iter = Fastq.iterate(options.stdin)
for record in iter:
c.input += 1
outfile_seq.write(">%s\n%s\n" % (record.identifier, record.seq))
outfile_qual.write(">%s\n%s\n" % (record.identifier, record.quals))
c.output += 1
outfile_seq.close()
outfile_qual.close()
# write footer and output benchmark information.
E.info("%s" % str(c))
E.stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("--split-barcode", dest="split", action="store_true",
help="barcode is split across read pair")
parser.add_option("-p", "--bc-pattern", dest="pattern", type="string",
help="Barcode pattern. Ns are random bases X's fixed")
parser.add_option("--bc-pattern2", dest="pattern2", type="string",
help="Barcode pattern. Ns are random bases X's fixed")
parser.add_option("--read2-in", dest="read2_in", type="string",
help="file name for read pairs")
parser.add_option("--3prime", dest="prime3", action="store_true",
help="barcode is on 3' end of read")
parser.add_option("--read2-out", dest="read2_out", type="string",
help="file to output processed paired read to")
parser.add_option("--supress-stats", dest="stats", action="store_false",
help="Suppress the writing of stats to the log")
parser.set_defaults(split=False,
pattern=None,
pattern2=None,
read2_in=None,
read2_out=None,
prime3=False,
stats=True)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
# check options
if not options.pattern:
raise ValueError("must specify a pattern using ``--bc-pattern``")
if options.split:
if not options.read2_in:
raise ValueError("must specify a paired fastq ``--read2-in``")
if not options.pattern2:
options.pattern2 = options.pattern
if options.read2_in:
if not options.read2_out:
raise ValueError("must specify an output for the paired end "
"``--read2-out``")
# Initialise the processor
processor = Extractor(options.pattern, options.pattern2, options.prime3)
read1s = Fastq.iterate(options.stdin)
if options.read2_in is None:
for read in read1s:
options.stdout.write(str(processor(read)) + "\n")
else:
read2s = Fastq.iterate(IOTools.openFile(options.read2_in))
read2_out = IOTools.openFile(options.read2_out, "w")
for read1, read2 in zip(read1s, read2s):
new_1, new_2 = processor(read1, read2)
options.stdout.write(str(new_1) + "\n")
read2_out.write(str(new_2) + "\n")
# write footer and output benchmark information.
if options.stats:
options.stdlog.write("\t".join(["Barcode", "UMI", "Sample", "Count"]) + "\n")
for id in processor.bc_count:
options.stdlog.write("\t".join(id+(str(processor.bc_count[id]),)) + "\n")
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-m", "--method", dest="method", type="choice",
choices=(
"apply",
"change-format",
"renumber-reads",
"sample",
"sort",
"trim3",
"trim5",
"unique",
"grep"),
help="method to apply [%default]")
parser.add_option(
"--target-format", dest="target_format", type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer', 'illumina-1.8'),
help="guess quality score format and set quality scores "
"to format [default=%default].")
parser.add_option(
"--guess-format", dest="guess_format", type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer', 'illumina-1.8'),
help="quality score format to assume if ambiguous [default=%default].")
parser.add_option(
"--sample-size", dest="sample_size", type="float",
help="proportion of reads to sample. "
"Provide a proportion of reads to sample, e.g. 0.1 for 10%, "
"0.5 for 50%, etc [default=%default].")
parser.add_option(
"--pair-fastq-file", dest="pair", type="string",
help="if data is paired, filename with second pair. "
"Implemented for sampling [default=%default].")
parser.add_option(
"--map-tsv-file", dest="map_tsv_file", type="string",
help="filename with tab-separated identifiers mapping for "
"method apply [default=%default].")
parser.add_option(
"--num-bases", dest="nbases", type="int",
help="number of bases to trim [default=%default].")
parser.add_option(
"--seed", dest="seed", type="int",
help="seed for random number generator [default=%default].")
parser.add_option(
"--pattern-identifier", dest="renumber_pattern", type="string",
help="rename reads in file by pattern [default=%default]")
parser.add_option(
"--grep-pattern", dest="grep_pattern", type="string",
help="subset to reads matching pattern [default=%default]")
parser.set_defaults(
method=None,
change_format=None,
guess_format=None,
sample_size=0.1,
nbases=0,
pair=None,
apply=None,
seed=None,
renumber_pattern="read_%010i",
grep_pattern=".*")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv, add_output_options=True)
c = E.Counter()
if options.method == "change-format":
for record in Fastq.iterate_convert(options.stdin,
format=options.target_format,
guess=options.guess_format):
c.input += 1
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "grep":
for record in Fastq.iterate(options.stdin):
if re.match(options.grep_pattern, record.seq):
options.stdout.write("%s\n" % record)
elif options.method == "sample":
sample_threshold = min(1.0, options.sample_size)
random.seed(options.seed)
if options.pair:
if not options.output_filename_pattern:
raise ValueError(
"please specify output filename pattern for "
"second pair (--output-filename-pattern)")
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.outfile_filename_pattern, "w")
for record1, record2 in itertools.izip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.openFile(options.pair))):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
outfile1.write("%s\n" % record1)
outfile2.write("%s\n" % record2)
for record in Fastq.iterate(options.stdin):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.method == "apply":
ids = set(IOTools.readList(IOTools.openFile(options.apply)))
for record in Fastq.iterate(options.stdin):
c.input += 1
if re.sub(" .*", "", record.identifier).strip() in ids:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.method == "trim3":
trim3 = options.nbases
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim(trim3)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "trim5":
trim5 = options.nbases
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim5(trim5)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "unique":
keys = set()
for record in Fastq.iterate(options.stdin):
c.input += 1
if record.identifier in keys:
continue
else:
keys.add(record.identifier)
options.stdout.write("%s\n" % record)
c.output += 1
# Need to change this to incorporate both pairs
elif options.method == "sort":
if not options.pair:
# This is quicker for a single fastq file
statement = "paste - - - - | sort -k1,1 -t ' ' | tr '\t' '\n'"
os.system(statement)
else:
if not options.output_filename_pattern:
raise ValueError(
"please specify output filename for second pair "
"(--output-filename-pattern)")
E.warn(
"consider sorting individual fastq files - "
"this is memory intensive")
entries1 = {}
entries2 = {}
for record1, record2 in itertools.izip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.openFile(options.pair))):
entries1[
record1.identifier[:-2]] = (record1.seq, record1.quals)
entries2[
record2.identifier[:-2]] = (record2.seq, record2.quals)
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.output_filename_pattern, "w")
assert len(set(entries1.keys()).intersection(
set(entries2.keys()))) == len(entries1),\
"paired files do not contain the same reads "\
"need to reconcile files"
for entry in sorted(entries1):
outfile1.write("@%s/1\n%s\n+\n%s\n" %
(entry, entries1[entry][0], entries1[entry][1]))
outfile2.write("@%s/2\n%s\n+\n%s\n" %
(entry, entries2[entry][0], entries2[entry][1]))
elif options.method == "renumber-reads":
id_count = 1
for record in Fastq.iterate(options.stdin):
record.identifier = options.renumber_pattern % id_count
id_count += 1
options.stdout.write("@%s\n%s\n+\n%s\n" %
(record.identifier, record.seq, record.quals))
# write footer and output benchmark information.
E.info("%s" % str(c))
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-m", "--method", dest="method", type="choice",
choices=('join', ),
help="method to apply [default=%default].")
parser.set_defaults(
method="join",
)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if len(args) != 2:
raise ValueError(
"please supply at least two fastq files on the commandline")
fn1, fn2 = args
c = E.Counter()
outfile = options.stdout
if options.method == "join":
# merge based on diagonals in dotplot
iter1 = Fastq.iterate(IOTools.openFile(fn1))
iter2 = Fastq.iterate(IOTools.openFile(fn2))
tuple_size = 2
for left, right in zip(iter1, iter2):
c.input += 1
# build dictionary of tuples
s1, q1 = left.seq, left.quals
d = collections.defaultdict(list)
for x in range(len(s1) - tuple_size):
d[s1[x:x + tuple_size]].append(x)
s2, q2 = right.seq, right.quals
# reverse complement
s2 = Genomics.complement(s2)
q2 = q2[::-1]
# compute list of offsets/diagonals
offsets = collections.defaultdict(int)
for x in range(len(s2) - tuple_size):
c = s2[x:x + tuple_size]
for y in d[c]:
offsets[x - y] += 1
# find maximum diagonal
sorted = sorted([(y, x) for x, y in offsets.items()])
max_count, max_offset = sorted[-1]
E.debug('%s: maximum offset at %i' % (left.identifier,
max_offset))
# simple merge sequence
take = len(s2) - max_offset
merged_seq = s1 + s2[take:]
# simple merge quality scores
merged_quals = q1 + q2[take:]
new_entry = copy.copy(left)
new_entry.seq = merged_seq
new_entry.quals = merged_quals
outfile.write(new_entry)
c.output += 1
# write footer and output benchmark information.
E.info("%s" % str(c))
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-m",
"--method",
dest="method",
type="choice",
choices=("apply", "change-format", "renumber-reads",
"sample", "sort", "trim3", "trim5", "unique",
"grep"),
help="method to apply [%default]")
parser.add_option("--target-format",
dest="target_format",
type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer',
'illumina-1.8'),
help="guess quality score format and set quality scores "
"to format [default=%default].")
parser.add_option(
"--guess-format",
dest="guess_format",
type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer', 'illumina-1.8'),
help="quality score format to assume if ambiguous [default=%default].")
parser.add_option(
"--sample-size",
dest="sample_size",
type="float",
help="proportion of reads to sample. "
"Provide a proportion of reads to sample, e.g. 0.1 for 10%, "
"0.5 for 50%, etc [default=%default].")
parser.add_option("--pair-fastq-file",
dest="pair",
type="string",
help="if data is paired, filename with second pair. "
"Implemented for sampling [default=%default].")
parser.add_option(
"--map-tsv-file",
dest="map_tsv_file",
type="string",
help="filename with tab-separated identifiers mapping for "
"method apply [default=%default].")
parser.add_option("--num-bases",
dest="nbases",
type="int",
help="number of bases to trim [default=%default].")
parser.add_option(
"--seed",
dest="seed",
type="int",
help="seed for random number generator [default=%default].")
parser.add_option(
"--pattern-identifier",
dest="renumber_pattern",
type="string",
help="rename reads in file by pattern [default=%default]")
parser.add_option(
"--grep-pattern",
dest="grep_pattern",
type="string",
help="subset to reads matching pattern [default=%default]")
parser.set_defaults(method=None,
change_format=None,
guess_format=None,
sample_size=0.1,
nbases=0,
pair=None,
apply=None,
seed=None,
renumber_pattern="read_%010i",
grep_pattern=".*")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv, add_output_options=True)
c = E.Counter()
if options.method == "change-format":
for record in Fastq.iterate_convert(options.stdin,
format=options.target_format,
guess=options.guess_format):
c.input += 1
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "grep":
for record in Fastq.iterate(options.stdin):
if re.match(options.grep_pattern, record.seq):
options.stdout.write("%s\n" % record)
elif options.method == "sample":
sample_threshold = min(1.0, options.sample_size)
random.seed(options.seed)
if options.pair:
if not options.output_filename_pattern:
raise ValueError("please specify output filename pattern for "
"second pair (--output-filename-pattern)")
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.output_filename_pattern, "w")
for record1, record2 in itertools.izip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.openFile(options.pair))):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
outfile1.write("%s\n" % record1)
outfile2.write("%s\n" % record2)
else:
for record in Fastq.iterate(options.stdin):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.method == "apply":
ids = set(IOTools.readList(IOTools.openFile(options.apply)))
for record in Fastq.iterate(options.stdin):
c.input += 1
if re.sub(" .*", "", record.identifier).strip() in ids:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.method == "trim3":
trim3 = options.nbases
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim(trim3)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "trim5":
trim5 = options.nbases
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim5(trim5)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.method == "unique":
keys = set()
for record in Fastq.iterate(options.stdin):
c.input += 1
if record.identifier in keys:
continue
else:
keys.add(record.identifier)
options.stdout.write("%s\n" % record)
c.output += 1
# Need to change this to incorporate both pairs
elif options.method == "sort":
if not options.pair:
# This is quicker for a single fastq file
statement = "paste - - - - | sort -k1,1 -t ' ' | tr '\t' '\n'"
os.system(statement)
else:
if not options.output_filename_pattern:
raise ValueError(
"please specify output filename for second pair "
"(--output-filename-pattern)")
E.warn("consider sorting individual fastq files - "
"this is memory intensive")
entries1 = {}
entries2 = {}
for record1, record2 in itertools.izip(
Fastq.iterate(options.stdin),
Fastq.iterate(IOTools.openFile(options.pair))):
entries1[record1.identifier[:-2]] = (record1.seq,
record1.quals)
entries2[record2.identifier[:-2]] = (record2.seq,
record2.quals)
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.output_filename_pattern, "w")
assert len(set(entries1.keys()).intersection(
set(entries2.keys()))) == len(entries1),\
"paired files do not contain the same reads "\
"need to reconcile files"
for entry in sorted(entries1):
outfile1.write("@%s/1\n%s\n+\n%s\n" %
(entry, entries1[entry][0], entries1[entry][1]))
outfile2.write("@%s/2\n%s\n+\n%s\n" %
(entry, entries2[entry][0], entries2[entry][1]))
elif options.method == "renumber-reads":
id_count = 1
for record in Fastq.iterate(options.stdin):
record.identifier = options.renumber_pattern % id_count
id_count += 1
options.stdout.write("@%s\n%s\n+\n%s\n" %
(record.identifier, record.seq, record.quals))
# write footer and output benchmark information.
E.info("%s" % str(c))
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id: cgat_script_template.py 2871 2010-03-03 10:20:44Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-f", "--change-format", dest="change_format", type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer', 'illumina-1.8'),
help="guess quality score format and set quality scores to format [default=%default].")
parser.add_option("--guess-format", dest="guess_format", type="choice",
choices=('sanger', 'solexa', 'phred64', 'integer', 'illumina-1.8'),
help="quality score format to assume if ambiguous [default=%default].")
parser.add_option("--sample", dest="sample", type="float",
help="sample a proportion of reads [default=%default].")
parser.add_option("--pair", dest="pair", type="string",
help="if data is paired, filename with second pair. "
"Implemented for sampling [default=%default].")
parser.add_option("--outfile-pair", dest="outfile_pair", type="string",
help="if data is paired, filename for second pair. "
"Implemented for sampling [default=%default].")
parser.add_option("--uniq", dest="uniq", action="store_true",
help="remove duplicate reads (by name) [default=%default].")
parser.add_option("--apply", dest="apply", type="string",
help="apply a filter to fastq file (taking only reads in filename) [default=%default].")
parser.add_option("--trim3", dest="trim3", type="int",
help="trim # bases from 3' end [default=%default].")
parser.add_option("--sort", dest="sort", action="store_true",
help="sort fastq by sequence id [default=%default].")
parser.add_option("--seed", dest="seed", type="int",
help="seed for random number generator [default=%default].")
parser.add_option("--renumber-ids", dest="renumber_ids", type="string",
help="rename reads in file by pattern [default=%default]")
parser.set_defaults(
change_format=None,
guess_format=None,
sample=None,
trim3=None,
pair=None,
apply=None,
uniq=False,
outfile_pair=None,
sort=None,
seed=None,
renumber_ids=None)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
c = E.Counter()
if options.change_format:
for record in Fastq.iterate_convert(options.stdin,
format=options.change_format,
guess=options.guess_format):
c.input += 1
options.stdout.write("%s\n" % record)
c.output += 1
elif options.sample:
sample_threshold = min(1.0, options.sample)
random.seed(options.seed)
if options.pair:
if not options.outfile_pair:
raise ValueError(
"please specify output filename for second pair (--outfile-pair)")
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.outfile_pair, "w")
for record1, record2 in itertools.izip(Fastq.iterate(options.stdin), Fastq.iterate(IOTools.openFile(options.pair))):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
outfile1.write("%s\n" % record1)
outfile2.write("%s\n" % record2)
for record in Fastq.iterate(options.stdin):
c.input += 1
if random.random() <= sample_threshold:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.apply:
ids = set(IOTools.readList(IOTools.openFile(options.apply)))
for record in Fastq.iterate(options.stdin):
c.input += 1
if re.sub(" .*", "", record.identifier).strip() in ids:
c.output += 1
options.stdout.write("%s\n" % record)
elif options.trim3:
trim3 = options.trim3
for record in Fastq.iterate(options.stdin):
c.input += 1
record.trim(trim3)
options.stdout.write("%s\n" % record)
c.output += 1
elif options.uniq:
keys = set()
for record in Fastq.iterate(options.stdin):
c.input += 1
if record.identifier in keys:
continue
else:
keys.add(record.identifier)
options.stdout.write("%s\n" % record)
c.output += 1
# Need to change this to incorporate both pairs
elif options.sort:
if not options.pair:
# This is quicker for a single fastq file
statement = "paste - - - - | sort -k1,1 -t ' ' | tr '\t' '\n'"
os.system(statement)
else:
if not options.outfile_pair:
raise ValueError(
"please specify output filename for second pair (--outfile-pair)")
E.warn(
"consider sorting individual fastq files - this is memory intensive")
entries1 = {}
entries2 = {}
for record1, record2 in itertools.izip(Fastq.iterate(options.stdin), Fastq.iterate(IOTools.openFile(options.pair))):
entries1[
record1.identifier[:-2]] = (record1.seq, record1.quals)
entries2[
record2.identifier[:-2]] = (record2.seq, record2.quals)
outfile1 = options.stdout
outfile2 = IOTools.openFile(options.outfile_pair, "w")
assert len(set(entries1.keys()).intersection(set(entries2.keys()))) == len(entries1), """paired files do not contain the same reads
need to reconcile files"""
for entry in sorted(entries1):
outfile1.write("@%s/1\n%s\n+\n%s\n" %
(entry, entries1[entry][0], entries1[entry][1]))
outfile2.write("@%s/2\n%s\n+\n%s\n" %
(entry, entries2[entry][0], entries2[entry][1]))
elif options.renumber_ids:
id_count = 1
for record in Fastq.iterate(options.stdin):
record.identifier = options.renumber_ids % id_count
id_count += 1
options.stdout.write("@%s\n%s\n+\n%s\n" %
(record.identifier, record.seq, record.quals))
# write footer and output benchmark information.
E.info("%s" % str(c))
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-p", "--bc-pattern", dest="pattern", type="string",
help="Barcode pattern. Ns are random bases X's fixed")
parser.add_option("--read2-in", dest="read2_in", type="string",
help="file name for read pairs")
parser.add_option("--3prime", dest="prime3", action="store_true",
help="barcode is on 3' end of read")
parser.add_option("--read2-out", dest="read2_out", type="string",
help="file to output processed paired read to")
parser.add_option("--supress-stats", dest="stats", action="store_false",
help="Suppress the writing of stats to the log")
parser.set_defaults(pattern=None,
read2_in=None,
read2_out=None,
prime3=False,
stats=True)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
#Initialise the processor
processor = Extractor(options.pattern, options.prime3)
read1s = Fastq.iterate(options.stdin)
if options.read2_in is None:
for read in read1s:
options.stdout.write(str(processor(read)) + "\n")
else:
read2s = Fastq.iterate(IOTools.openFile(options.read2_in))
read2_out = IOTools.openFile(options.read2_out)
for read1, read2 in zip(read1s, read2s):
new_1, new_2 = processor(read1, read2)
options.stdout.write(str(new_1) + "\n")
read2_out.write(str(new_2) + "\n")
# write footer and output benchmark information.
if options.stats:
options.stdlog.write("\t".join(["Barcode", "UMI", "Sample", "Count"]) + "\n")
for id in processor.bc_count:
options.stdlog.write("\t".join(id+(str(processor.bc_count[id]),)) + "\n")
E.Stop()
