def buildVariantSequences(indexed_variants, sequences):
'''build variant sequences by inserting ``variants`` into ``sequences``.
For each sequence, two alleles are returned. Both alleles are initialized
as wildtype sequences. In the absence of any phasing information, variants
are preferably added to the second allele, such that the wild-type status
of the first allele is preserved as much as possible
returns a dictionary of lists.
'''
result = {}
for key, sequence in sequences.iteritems():
feature_start, feature_end = key
variants = [
(x, y,) + z for (x, y, z) in indexed_variants.find(feature_start, feature_end)]
allele1, allele2 = Variants.buildAlleles(sequence,
variants,
reference_start=feature_start)
result[(feature_start, feature_end)] = (allele1, allele2)
return result
def buildVariantSequences(indexed_variants, sequences):
'''build variant sequences by inserting ``variants`` into ``sequences``.
For each sequence, two alleles are returned. Both alleles are initialized
as wildtype sequences. In the absence of any phasing information, variants
are preferably added to the second allele, such that the wild-type status
of the first allele is preserved as much as possible
returns a dictionary of lists.
'''
result = {}
for key, sequence in sequences.items():
feature_start, feature_end = key
variants = [(
x,
y,
) + z for (x, y,
z) in indexed_variants.find(feature_start, feature_end)]
allele1, allele2 = Variants.buildAlleles(sequence,
variants,
reference_start=feature_start)
result[(feature_start, feature_end)] = (allele1, allele2)
return result
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: snp2maf.py 2875 2010-03-27 17:42:04Z andreas $", usage=globals()["__doc__"])
parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome [default=%default].")
parser.add_option("-t", "--tracks", dest="tracks", type="string", action="append",
help="tracks (tablenames) to use in sqlite database [default=%default].")
parser.add_option("-d", "--database", dest="database", type="string",
help="sqlite3 database [default=%default].")
parser.add_option("-r", "--reference", dest="reference", type="string",
help="name of reference [default=%default].")
parser.add_option("-i", "--is-gtf", dest="is_gtf", action="store_true",
help="if set, the gene_id will be added to the alignment header [default=%default].")
parser.add_option("-z", "--compress", dest="compress", action="store_true",
help="compress output with gzip [default=%default].")
parser.add_option("-p", "--pattern-identifier", dest="pattern_track", type="string",
help="regular expression pattern for track [default=%default].")
parser.set_defaults(
genome_file=None,
tracks=[],
database="csvdb",
output=[],
border=0,
reference_name="reference",
pattern_track="(\S+)",
is_gtf=True,
compress=False,
)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv, add_output_options=True)
ninput, nskipped, noutput = 0, 0, 0
if not options.database or not options.tracks:
raise ValueError("please supply both database and tracks")
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
else:
fasta = None
if options.is_gtf:
infile_gff = GTF.iterator(options.stdin)
else:
infile_gff = GTF.iterator(options.stdin)
dbhandle = sqlite3.connect(options.database)
statement = '''SELECT pos, reference, genotype
FROM %(track)s
WHERE contig = '%(contig)s' AND
pos BETWEEN %(extended_start)s and %(extended_end)s
'''
counts = E.Counter()
tracks = options.tracks
try:
translated_tracks = [
re.search(options.pattern_track, track).groups()[0] for track in tracks]
except AttributeError:
raise AttributeError(
"pattern `%s` does not match input tracks." % options.pattern_track)
if options.compress:
outfile = gzip.GzipFile(fileobj=options.stdout)
else:
outfile = options.stdout
outfile.flush()
outfile.write("##maf version=1 program=snp2maf.py\n\n")
for gff in infile_gff:
counts.input += 1
contig = gff.contig
strand = gff.strand
lcontig = fasta.getLength(contig)
region_start, region_end = gff.start, gff.end
if contig.startswith("chr"):
contig = contig[3:]
extended_start = region_start - options.border
extended_end = region_end + options.border
is_positive = Genomics.IsPositiveStrand(strand)
E.info("processing %s" % str(gff))
# collect all variants
all_variants = []
for track in options.tracks:
cc = dbhandle.cursor()
cc.execute(statement % locals())
all_variants.append(map(Variants.Variant._make, cc.fetchall()))
cc.close()
E.debug("%s:%i..%i collected %i variants for %i tracks" % (contig,
region_start, region_end,
sum([
len(x) for x in all_variants]),
len(all_variants)))
reference_seq = fasta.getSequence(
contig, "+", region_start, region_end)
lseq = len(reference_seq)
alleles = collections.defaultdict(list)
# build allele sequences for track and count maximum chars per mali
# column
colcounts = numpy.ones(lseq)
for track, variants in zip(translated_tracks, all_variants):
variants = Variants.updateVariants(variants, lcontig, "+")
a = Variants.buildAlleles(reference_seq,
variants,
reference_start=region_start)
alleles[track] = a
for allele in a:
for pos, c in enumerate(allele):
colcounts[pos] = max(colcounts[pos], len(c))
# realign gapped regions
alignIndels(alleles, colcounts)
if options.is_gtf:
outfile.write("a gene_id=%s\n" % gff.gene_id)
else:
outfile.write("a\n")
maf_format = "s %(name)-30s %(pos)9i %(size)6i %(strand)s %(lcontig)9i %(seq)s\n"
def __addGaps(sequence, colcounts):
'''output gapped sequence.'''
r = []
for x, c in enumerate(sequence):
r.append(c + "-" * (colcounts[x] - len(c)))
return "".join(r)
name = ".".join((options.reference, contig))
if is_positive:
pos = region_start
else:
pos = lcontig - region_start
size = lseq
seq = __addGaps(reference_seq, colcounts)
outfile.write(maf_format % (locals()))
for track in translated_tracks:
for aid, allele in enumerate(alleles[track]):
seq = __addGaps(allele, colcounts)
if not is_positive:
Genomics.complement(seq)
size = len(seq) - seq.count("-")
name = ".".join((track + "-%i" % aid, contig))
outfile.write(maf_format % (locals()))
outfile.write("\n")
E.info("%s" % str(counts))
# 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: snp2maf.py 2875 2010-03-27 17:42:04Z andreas $", usage=globals()["__doc__"])
parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome [default=%default].")
parser.add_option("-t", "--tracks", dest="tracks", type="string", action="append",
help="tracks (tablenames) to use in sqlite database [default=%default].")
parser.add_option("-d", "--database", dest="database", type="string",
help="sqlite3 database [default=%default].")
parser.add_option("-r", "--reference", dest="reference", type="string",
help="name of reference [default=%default].")
parser.add_option("-i", "--is-gtf", dest="is_gtf", action="store_true",
help="if set, the gene_id will be added to the alignment header [default=%default].")
parser.add_option("-z", "--compress", dest="compress", action="store_true",
help="compress output with gzip [default=%default].")
parser.add_option("-p", "--pattern-identifier", dest="pattern_track", type="string",
help="regular expression pattern for track [default=%default].")
parser.set_defaults(
genome_file=None,
tracks=[],
database="csvdb",
output=[],
border=0,
reference_name="reference",
pattern_track="(\S+)",
is_gtf=True,
compress=False,
)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv, add_output_options=True)
ninput, nskipped, noutput = 0, 0, 0
if not options.database or not options.tracks:
raise ValueError("please supply both database and tracks")
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
else:
fasta = None
if options.is_gtf:
infile_gff = GTF.iterator(options.stdin)
else:
infile_gff = GTF.iterator(options.stdin)
dbhandle = sqlite3.connect(options.database)
statement = '''SELECT pos, reference, genotype
FROM %(track)s
WHERE contig = '%(contig)s' AND
pos BETWEEN %(extended_start)s and %(extended_end)s
'''
counts = E.Counter()
tracks = options.tracks
try:
translated_tracks = [
re.search(options.pattern_track, track).groups()[0] for track in tracks]
except AttributeError:
raise AttributeError(
"pattern `%s` does not match input tracks." % options.pattern_track)
if options.compress:
outfile = gzip.GzipFile(fileobj=options.stdout)
else:
outfile = options.stdout
outfile.flush()
outfile.write("##maf version=1 program=snp2maf.py\n\n")
for gff in infile_gff:
counts.input += 1
contig = gff.contig
strand = gff.strand
lcontig = fasta.getLength(contig)
region_start, region_end = gff.start, gff.end
if contig.startswith("chr"):
contig = contig[3:]
extended_start = region_start - options.border
extended_end = region_end + options.border
is_positive = Genomics.IsPositiveStrand(strand)
E.info("processing %s" % str(gff))
# collect all variants
all_variants = []
for track in options.tracks:
cc = dbhandle.cursor()
cc.execute(statement % locals())
all_variants.append(list(map(Variants.Variant._make, cc.fetchall())))
cc.close()
E.debug("%s:%i..%i collected %i variants for %i tracks" % (contig,
region_start, region_end,
sum([
len(x) for x in all_variants]),
len(all_variants)))
reference_seq = fasta.getSequence(
contig, "+", region_start, region_end)
lseq = len(reference_seq)
alleles = collections.defaultdict(list)
# build allele sequences for track and count maximum chars per mali
# column
colcounts = numpy.ones(lseq)
for track, variants in zip(translated_tracks, all_variants):
variants = Variants.updateVariants(variants, lcontig, "+")
a = Variants.buildAlleles(reference_seq,
variants,
reference_start=region_start)
alleles[track] = a
for allele in a:
for pos, c in enumerate(allele):
colcounts[pos] = max(colcounts[pos], len(c))
# realign gapped regions
alignIndels(alleles, colcounts)
if options.is_gtf:
outfile.write("a gene_id=%s\n" % gff.gene_id)
else:
outfile.write("a\n")
maf_format = "s %(name)-30s %(pos)9i %(size)6i %(strand)s %(lcontig)9i %(seq)s\n"
def __addGaps(sequence, colcounts):
'''output gapped sequence.'''
r = []
for x, c in enumerate(sequence):
r.append(c + "-" * (colcounts[x] - len(c)))
return "".join(r)
name = ".".join((options.reference, contig))
if is_positive:
pos = region_start
else:
pos = lcontig - region_start
size = lseq
seq = __addGaps(reference_seq, colcounts)
outfile.write(maf_format % (locals()))
for track in translated_tracks:
for aid, allele in enumerate(alleles[track]):
seq = __addGaps(allele, colcounts)
if not is_positive:
Genomics.complement(seq)
size = len(seq) - seq.count("-")
name = ".".join((track + "-%i" % aid, contig))
outfile.write(maf_format % (locals()))
outfile.write("\n")
E.info("%s" % str(counts))
# write footer and output benchmark information.
E.stop()