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: gtf2alleles.py 2886 2010-04-07 08:47:46Z 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", "--tablename", dest="tablename", type="string",
help="tablename to get variants from (in samtools pileup format) [default=%default].")
parser.add_option("-d", "--database", dest="database", type="string",
help="sqlite3 database [default=%default].")
parser.add_option("-f", "--exons-file", dest="filename_exons", type="string",
help="filename with transcript model information (gtf formatted file) [default=%default].")
parser.add_option("-r", "--filename-reference", dest="filename_reference", type="string",
help="filename with transcript models of a reference gene set. Stop codons that do not"
" overlap any of the exons in this file are ignore (gtf-formatted file) [default=%default].")
parser.add_option("--vcf-file", dest="filename_vcf", type="string",
help="filename with variants in VCF format. Should be indexed by tabix [default=%default].")
parser.add_option("--pileup-file", dest="filename_pileup", type="string",
help="filename with variants in samtools pileup format. Should be indexed by tabix [default=%default].")
parser.add_option("--vcf-sample", dest="vcf_sample", type="string",
help="sample id for species of interest in vcf formatted file [default=%default].")
parser.add_option("-s", "--seleno-tsv-file", dest="filename_seleno", type="string",
help="filename of a list of transcript ids that are selenoproteins [default=%default].")
parser.add_option("-m", "--module", dest="modules", type="choice", action="append",
choices=("gene-counts", "transcript-effects"),
help="modules to apply [default=%default].")
parser.add_option("-o", "--output-section", dest="output", type="choice", action="append",
choices=("all", "peptide", "cds", "table", "gtf", "map"),
help="sections to output [default=%default].")
parser.add_option("-k", "--with-knockouts", dest="with_knockouts", action="store_true",
help="add alleles that are knocked out to fasta and gtf files [default=%default].")
parser.set_defaults(
genome_file=None,
filename_exons=None,
filename_referenec=None,
filename_seleno=None,
modules=[],
border=200,
separator="|",
tablename=None,
database="csvdb",
output=[],
with_knockouts=False,
filename_vcf=None,
vcf_sample=None,
)
# 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 options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
else:
fasta = None
if options.filename_seleno:
seleno = set(IOTools.readList(open(options.filename_seleno, "r")))
else:
seleno = {}
infile_gtf = GTF.gene_iterator(GTF.iterator(options.stdin))
# acquire variants from SQLlite database
if options.tablename:
if not options.database:
raise ValueError("please supply both database and tablename")
variant_getter = VariantGetterSqlite(
options.database, options.tablename)
elif options.filename_pileup:
variant_getter = VariantGetterPileup(options.filename_pileup)
elif options.filename_vcf:
variant_getter = VariantGetterVCF(
options.filename_vcf, options.vcf_sample)
else:
raise ValueError("please specify a source of variants.")
if len(options.output) == 0 or "all" in options.output:
output_all = True
else:
output_all = False
if "cds" in options.output or output_all:
outfile_cds = E.openOutputFile("cds.fasta")
else:
outfile_cds = None
if "map" in options.output or output_all:
outfile_map = E.openOutputFile("map.psl")
else:
outfile_map = None
if "peptide" in options.output or output_all:
outfile_peptides = E.openOutputFile("peptides.fasta")
else:
outfile_peptides = None
if "table" in options.output or output_all:
outfile_alleles = E.openOutputFile("table")
outfile_alleles.write("\t".join(
("gene_id",
"transcript_id", "allele_id", "contig", "strand",
"is_wildtype",
("\t".join(Allele._fields)))) + "\n")
else:
outfile_alleles = None
if "gtf" in options.output or output_all:
outfile_gtf = E.openOutputFile("gtf")
else:
outfile_gtf = None
# id separatar
separator = options.separator
for transcripts in infile_gtf:
gene_id = transcripts[0][0].gene_id
overall_start = min([min([x.start for x in y]) for y in transcripts])
overall_end = max([max([x.end for x in y]) for y in transcripts])
contig = transcripts[0][0].contig
strand = transcripts[0][0].strand
is_positive_strand = Genomics.IsPositiveStrand(strand)
lcontig = fasta.getLength(contig)
E.info("%s: started processing on %s:%i..%i (%s)" %
(gene_id, contig, overall_start, overall_end, strand))
ninput += 1
extended_start = max(0, overall_start - options.border)
extended_end = min(lcontig, overall_end + options.border)
# if contig.startswith("chr"): contig = contig[3:]
variants = variant_getter(contig, extended_start, extended_end)
E.debug("%s: found %i variants in %s:%i..%i" %
(gene_id, len(variants), contig, extended_start, extended_end))
if E.global_options.loglevel >= 10:
print "# collected variants:", variants
# collect intron/exon sequences
# coordinates are forward/reverse
# also updates the coordinates in transcripts
all_exons, all_introns = collectExonIntronSequences(transcripts, fasta)
# update variants such that they use the same coordinates
# as the transcript
variants = Variants.updateVariants(variants, lcontig, strand)
# deal with overlapping but consistent variants
variants = Variants.mergeVariants(variants)
E.debug("%s: found %i variants after merging in %s:%i..%i" %
(gene_id, len(variants), contig, extended_start, extended_end))
if E.global_options.loglevel >= 10:
print "# merged variants:", variants
# collect coordinate offsets and remove conflicting variants
variants, removed_variants, offsets = Variants.buildOffsets(
variants, contig=contig)
if len(removed_variants) > 0:
E.warn("removed %i conflicting variants" % len(removed_variants))
for v in removed_variants:
E.info("removed variant: %s" % str(v))
E.info("%i variants after filtering" % len(variants))
if len(variants) > 0:
# build variants
indexed_variants = Variants.indexVariants(variants)
# update exon sequences according to variants
variant_exons = buildVariantSequences(indexed_variants, all_exons)
# update intron sequences according to variants
variant_introns = buildVariantSequences(
indexed_variants, all_introns)
if E.global_options.loglevel >= 10:
for key in variant_exons:
print "exon", key
Genomics.printPrettyAlignment(
all_exons[key],
variant_exons[key][0],
variant_exons[key][1],
)
for key in variant_introns:
print "intron", key
Genomics.printPrettyAlignment(
all_introns[key][:30] + all_introns[key][-30:],
variant_introns[key][0][:30] +
variant_introns[key][0][-30:],
variant_introns[key][1][:30] + variant_introns[key][1][-30:])
else:
variant_exons, variant_introns = None, None
for transcript in transcripts:
transcript.sort(key=lambda x: x.start)
transcript_id = transcript[0].transcript_id
alleles = buildAlleles(transcript,
variant_exons,
variant_introns,
all_exons,
all_introns,
offsets,
is_seleno=transcript_id in seleno,
reference_coordinates=False,
)
##############################################################
##############################################################
##############################################################
# output
for aid, al in enumerate(alleles):
allele, map_cds2reference = al
reference_cds_sequence = buildCDSSequence(
transcript, all_exons)
is_wildtype = reference_cds_sequence == allele.cds
allele_id = str(aid)
assert len(allele.exon_starts) == allele.nexons
assert len(allele.cds_starts) == allele.nexons
assert len(allele.frames) == allele.nexons
# the output id
outid = separator.join((gene_id, transcript_id, allele_id))
# output map between cds and reference
if outfile_map and map_cds2reference:
match = Blat.Match()
match.mQueryId = allele_id
match.mQueryLength = allele.cds_len
match.mSbjctId = contig
match.mSbjctLength = lcontig
match.strand = strand
match.fromMap(map_cds2reference, use_strand=True)
outfile_map.write("%s\n" % str(match))
# only output sequences for genes that have not been knocked
# out, unless required
if not allele.is_nmd_knockout or options.with_knockouts:
if outfile_gtf:
gtf = GTF.Entry()
gtf.gene_id = gene_id
gtf.transcript_id = transcript_id
gtf.addAttribute("allele_id", allele_id)
gtf.contig = contig
gtf.strand = strand
gtf.feature = "CDS"
gtf.source = "gtfxnsps"
l = 0
last_cds_start = allele.cds_starts[0]
gtf.start = allele.exon_starts[0]
gtf.frame = allele.frames[0]
for exon_start, cds_start, frame in zip(allele.exon_starts[1:],
allele.cds_starts[
1:],
allele.frames[1:]):
cds_length = cds_start - last_cds_start
gtf.end = gtf.start + cds_length
if not is_positive_strand:
gtf.start, gtf.end = lcontig - \
gtf.end, lcontig - gtf.start
outfile_gtf.write(str(gtf) + "\n")
gtf.start = exon_start
gtf.frame = frame
l += cds_length
last_cds_start = cds_start
cds_length = len(allele.cds) - last_cds_start
gtf.end = gtf.start + cds_length
if not is_positive_strand:
gtf.start, gtf.end = lcontig - \
gtf.end, lcontig - gtf.start
outfile_gtf.write(str(gtf) + "\n")
if outfile_cds:
outfile_cds.write(">%s\n%s\n" % (outid, allele.cds))
if outfile_peptides:
outfile_peptides.write(
">%s\n%s\n" % (outid, allele.peptide))
# reformat for tabular output
allele = allele._replace(
cds_starts=",".join(map(str, allele.cds_starts)),
exon_starts=",".join(map(str, allele.exon_starts)),
frames=",".join(map(str, allele.frames)))
# convert reference coordinates to positive strand coordinates
if allele.reference_first_stop_start >= 0 and not is_positive_strand:
allele = allele._replace(
reference_first_stop_start=lcontig -
allele.reference_first_stop_end,
reference_first_stop_end=lcontig - allele.reference_first_stop_start, )
if outfile_alleles:
outfile_alleles.write("%s\t%s\n" % (
"\t".join((gene_id,
transcript_id,
allele_id,
contig,
strand,
"%i" % is_wildtype)),
"\t".join(map(str, allele))))
noutput += 1
# only output first allele (debugging)
# break
E.info("ninput=%i, noutput=%i, nskipped=%i" % (ninput, noutput, nskipped))
# 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(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: gtf2alleles.py 2886 2010-04-07 08:47:46Z 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",
"--tablename",
dest="tablename",
type="string",
help=
"tablename to get variants from (in samtools pileup format) [default=%default]."
)
parser.add_option("-d",
"--database",
dest="database",
type="string",
help="sqlite3 database [default=%default].")
parser.add_option(
"-f",
"--exons-file",
dest="filename_exons",
type="string",
help=
"filename with transcript model information (gtf formatted file) [default=%default]."
)
parser.add_option(
"-r",
"--filename-reference",
dest="filename_reference",
type="string",
help=
"filename with transcript models of a reference gene set. Stop codons that do not"
" overlap any of the exons in this file are ignore (gtf-formatted file) [default=%default]."
)
parser.add_option(
"--vcf-file",
dest="filename_vcf",
type="string",
help=
"filename with variants in VCF format. Should be indexed by tabix [default=%default]."
)
parser.add_option(
"--pileup-file",
dest="filename_pileup",
type="string",
help=
"filename with variants in samtools pileup format. Should be indexed by tabix [default=%default]."
)
parser.add_option(
"--vcf-sample",
dest="vcf_sample",
type="string",
help=
"sample id for species of interest in vcf formatted file [default=%default]."
)
parser.add_option(
"-s",
"--seleno-tsv-file",
dest="filename_seleno",
type="string",
help=
"filename of a list of transcript ids that are selenoproteins [default=%default]."
)
parser.add_option("-m",
"--module",
dest="modules",
type="choice",
action="append",
choices=("gene-counts", "transcript-effects"),
help="modules to apply [default=%default].")
parser.add_option("-o",
"--output-section",
dest="output",
type="choice",
action="append",
choices=("all", "peptide", "cds", "table", "gtf", "map"),
help="sections to output [default=%default].")
parser.add_option(
"-k",
"--with-knockouts",
dest="with_knockouts",
action="store_true",
help=
"add alleles that are knocked out to fasta and gtf files [default=%default]."
)
parser.set_defaults(
genome_file=None,
filename_exons=None,
filename_referenec=None,
filename_seleno=None,
modules=[],
border=200,
separator="|",
tablename=None,
database="csvdb",
output=[],
with_knockouts=False,
filename_vcf=None,
vcf_sample=None,
)
# 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 options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
else:
fasta = None
if options.filename_seleno:
seleno = set(IOTools.readList(open(options.filename_seleno, "r")))
else:
seleno = {}
infile_gtf = GTF.gene_iterator(GTF.iterator(options.stdin))
# acquire variants from SQLlite database
if options.tablename:
if not options.database:
raise ValueError("please supply both database and tablename")
variant_getter = VariantGetterSqlite(options.database,
options.tablename)
elif options.filename_pileup:
variant_getter = VariantGetterPileup(options.filename_pileup)
elif options.filename_vcf:
variant_getter = VariantGetterVCF(options.filename_vcf,
options.vcf_sample)
else:
raise ValueError("please specify a source of variants.")
if len(options.output) == 0 or "all" in options.output:
output_all = True
else:
output_all = False
if "cds" in options.output or output_all:
outfile_cds = E.openOutputFile("cds.fasta")
else:
outfile_cds = None
if "map" in options.output or output_all:
outfile_map = E.openOutputFile("map.psl")
else:
outfile_map = None
if "peptide" in options.output or output_all:
outfile_peptides = E.openOutputFile("peptides.fasta")
else:
outfile_peptides = None
if "table" in options.output or output_all:
outfile_alleles = E.openOutputFile("table")
outfile_alleles.write("\t".join(("gene_id", "transcript_id",
"allele_id", "contig", "strand",
"is_wildtype",
("\t".join(Allele._fields)))) + "\n")
else:
outfile_alleles = None
if "gtf" in options.output or output_all:
outfile_gtf = E.openOutputFile("gtf")
else:
outfile_gtf = None
# id separatar
separator = options.separator
for transcripts in infile_gtf:
gene_id = transcripts[0][0].gene_id
overall_start = min([min([x.start for x in y]) for y in transcripts])
overall_end = max([max([x.end for x in y]) for y in transcripts])
contig = transcripts[0][0].contig
strand = transcripts[0][0].strand
is_positive_strand = Genomics.IsPositiveStrand(strand)
lcontig = fasta.getLength(contig)
E.info("%s: started processing on %s:%i..%i (%s)" %
(gene_id, contig, overall_start, overall_end, strand))
ninput += 1
extended_start = max(0, overall_start - options.border)
extended_end = min(lcontig, overall_end + options.border)
# if contig.startswith("chr"): contig = contig[3:]
variants = variant_getter(contig, extended_start, extended_end)
E.debug("%s: found %i variants in %s:%i..%i" %
(gene_id, len(variants), contig, extended_start, extended_end))
if E.global_options.loglevel >= 10:
print("# collected variants:", variants)
# collect intron/exon sequences
# coordinates are forward/reverse
# also updates the coordinates in transcripts
all_exons, all_introns = collectExonIntronSequences(transcripts, fasta)
# update variants such that they use the same coordinates
# as the transcript
variants = Variants.updateVariants(variants, lcontig, strand)
# deal with overlapping but consistent variants
variants = Variants.mergeVariants(variants)
E.debug("%s: found %i variants after merging in %s:%i..%i" %
(gene_id, len(variants), contig, extended_start, extended_end))
if E.global_options.loglevel >= 10:
print("# merged variants:", variants)
# collect coordinate offsets and remove conflicting variants
variants, removed_variants, offsets = Variants.buildOffsets(
variants, contig=contig)
if len(removed_variants) > 0:
E.warn("removed %i conflicting variants" % len(removed_variants))
for v in removed_variants:
E.info("removed variant: %s" % str(v))
E.info("%i variants after filtering" % len(variants))
if len(variants) > 0:
# build variants
indexed_variants = Variants.indexVariants(variants)
# update exon sequences according to variants
variant_exons = buildVariantSequences(indexed_variants, all_exons)
# update intron sequences according to variants
variant_introns = buildVariantSequences(indexed_variants,
all_introns)
if E.global_options.loglevel >= 10:
for key in variant_exons:
print("exon", key)
Genomics.printPrettyAlignment(
all_exons[key],
variant_exons[key][0],
variant_exons[key][1],
)
for key in variant_introns:
print("intron", key)
Genomics.printPrettyAlignment(
all_introns[key][:30] + all_introns[key][-30:],
variant_introns[key][0][:30] +
variant_introns[key][0][-30:],
variant_introns[key][1][:30] +
variant_introns[key][1][-30:])
else:
variant_exons, variant_introns = None, None
for transcript in transcripts:
transcript.sort(key=lambda x: x.start)
transcript_id = transcript[0].transcript_id
alleles = buildAlleles(
transcript,
variant_exons,
variant_introns,
all_exons,
all_introns,
offsets,
is_seleno=transcript_id in seleno,
reference_coordinates=False,
)
##############################################################
##############################################################
##############################################################
# output
for aid, al in enumerate(alleles):
allele, map_cds2reference = al
reference_cds_sequence = buildCDSSequence(
transcript, all_exons)
is_wildtype = reference_cds_sequence == allele.cds
allele_id = str(aid)
assert len(allele.exon_starts) == allele.nexons
assert len(allele.cds_starts) == allele.nexons
assert len(allele.frames) == allele.nexons
# the output id
outid = separator.join((gene_id, transcript_id, allele_id))
# output map between cds and reference
if outfile_map and map_cds2reference:
match = Blat.Match()
match.mQueryId = allele_id
match.mQueryLength = allele.cds_len
match.mSbjctId = contig
match.mSbjctLength = lcontig
match.strand = strand
match.fromMap(map_cds2reference, use_strand=True)
outfile_map.write("%s\n" % str(match))
# only output sequences for genes that have not been knocked
# out, unless required
if not allele.is_nmd_knockout or options.with_knockouts:
if outfile_gtf:
gtf = GTF.Entry()
gtf.gene_id = gene_id
gtf.transcript_id = transcript_id
gtf.addAttribute("allele_id", allele_id)
gtf.contig = contig
gtf.strand = strand
gtf.feature = "CDS"
gtf.source = "gtfxnsps"
l = 0
last_cds_start = allele.cds_starts[0]
gtf.start = allele.exon_starts[0]
gtf.frame = allele.frames[0]
for exon_start, cds_start, frame in zip(
allele.exon_starts[1:], allele.cds_starts[1:],
allele.frames[1:]):
cds_length = cds_start - last_cds_start
gtf.end = gtf.start + cds_length
if not is_positive_strand:
gtf.start, gtf.end = lcontig - \
gtf.end, lcontig - gtf.start
outfile_gtf.write(str(gtf) + "\n")
gtf.start = exon_start
gtf.frame = frame
l += cds_length
last_cds_start = cds_start
cds_length = len(allele.cds) - last_cds_start
gtf.end = gtf.start + cds_length
if not is_positive_strand:
gtf.start, gtf.end = lcontig - \
gtf.end, lcontig - gtf.start
outfile_gtf.write(str(gtf) + "\n")
if outfile_cds:
outfile_cds.write(">%s\n%s\n" % (outid, allele.cds))
if outfile_peptides:
outfile_peptides.write(">%s\n%s\n" %
(outid, allele.peptide))
# reformat for tabular output
allele = allele._replace(
cds_starts=",".join(map(str, allele.cds_starts)),
exon_starts=",".join(map(str, allele.exon_starts)),
frames=",".join(map(str, allele.frames)))
# convert reference coordinates to positive strand coordinates
if allele.reference_first_stop_start >= 0 and not is_positive_strand:
allele = allele._replace(
reference_first_stop_start=lcontig -
allele.reference_first_stop_end,
reference_first_stop_end=lcontig -
allele.reference_first_stop_start,
)
if outfile_alleles:
outfile_alleles.write("%s\t%s\n" % ("\t".join(
(gene_id, transcript_id, allele_id, contig, strand,
"%i" % is_wildtype)), "\t".join(map(str, allele))))
noutput += 1
# only output first allele (debugging)
# break
E.info("ninput=%i, noutput=%i, nskipped=%i" % (ninput, noutput, nskipped))
# 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()
