print E.GetHeader()
print E.GetParams()
last_exon = Exons.Exon()
contig_sizes = {}
if param_filename_contigs:
infile = open(param_filename_contigs, "r")
for line in infile:
if line[0] == "#": continue
sbjct_token, size = line[:-1].split("\t")[:2]
contig_sizes[sbjct_token] = int(size)
map_prediction2genome = alignlib_lite.makeAlignmentSet()
nexons, npairs = 0, 0
for line in sys.stdin:
if line[0] == "#": continue
this_exon = Exons.Exon()
this_exon.Read(line)
if this_exon.mSbjctStrand == "-":
this_exon.InvertGenomicCoordinates(
contig_sizes[this_exon.mSbjctToken])
nexons += 1
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option(
"-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome.")
parser.add_option(
"-o", "--is-forward-coordinates", dest="forward_coordinates",
action="store_true",
help="input uses forward coordinates.")
parser.add_option(
"-f", "--format", dest="format", type="choice",
choices=(
"default", "cds", "cdnas", "map", "gff", "intron-fasta", "exons"),
help="output format.")
parser.add_option(
"-r", "--reset-to-start", dest="reset_to_start", action="store_true",
help="move genomic coordinates to begin from 0.")
parser.add_option("--reset-query", dest="reset_query", action="store_true",
help="move peptide coordinates to begin from 0.")
parser.set_defaults(
genome_file=None,
forward_coordinates=False,
format="default",
reset_to_start=False,
reset_query=False)
(options, args) = E.Start(parser, add_pipe_options=True)
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
cds_id = 1
entry = PredictionParser.PredictionParserEntry()
fasta = IndexedFasta.IndexedFasta(options.genome_file)
ninput, noutput, nskipped, nerrors = 0, 0, 0, 0
for line in sys.stdin:
if line[0] == "#":
continue
if line.startswith("id"):
continue
ninput += 1
try:
entry.Read(line)
except ValueError, msg:
options.stdlog.write(
"# parsing failed with msg %s in line %s" % (msg, line))
nerrors += 1
continue
cds = Exons.Alignment2Exons(entry.mMapPeptide2Genome,
query_from=entry.mQueryFrom,
sbjct_from=entry.mSbjctGenomeFrom,
add_stop_codon=0)
for cd in cds:
cd.mSbjctToken = entry.mSbjctToken
cd.mSbjctStrand = entry.mSbjctStrand
if cds[-1].mGenomeTo != entry.mSbjctGenomeTo:
options.stdlog.write(
"# WARNING: discrepancy in exon calculation!!!\n")
for cd in cds:
options.stdlog.write("# %s\n" % str(cd))
options.stdlog.write("# %s\n" % entry)
lsequence = fasta.getLength(entry.mSbjctToken)
genomic_sequence = fasta.getSequence(entry.mSbjctToken,
entry.mSbjctStrand,
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo)
# deal with forward coordinates: convert them to negative strand
# coordinates
if options.forward_coordinates and \
entry.mSbjctStrand == "-":
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo = lsequence - \
entry.mSbjctGenomeTo, lsequence - entry.mSbjctGenomeFrom
for cd in cds:
cd.InvertGenomicCoordinates(lsequence)
# attach sequence to cds
for cd in cds:
start = cd.mGenomeFrom - entry.mSbjctGenomeFrom
end = cd.mGenomeTo - entry.mSbjctGenomeFrom
cd.mSequence = genomic_sequence[start:end]
# reset coordinates for query
if options.reset_to_start:
offset = entry.mPeptideFrom
for cd in cds:
cd.mPeptideFrom -= offset
cd.mPeptideTo -= offset
# play with coordinates
if options.reset_to_start:
offset = entry.mSbjctGenomeFrom
for cd in cds:
cd.mGenomeFrom -= offset
cd.mGenomeTo -= offset
else:
offset = 0
if options.format == "cds":
rank = 0
for cd in cds:
rank += 1
cd.mQueryToken = entry.mQueryToken
cd.mSbjctToken = entry.mSbjctToken
cd.mSbjctStrand = entry.mSbjctStrand
cd.mRank = rank
print str(cd)
if options.format == "exons":
rank = 0
for cd in cds:
rank += 1
options.stdout.write("\t".join(map(str, (entry.mPredictionId,
cd.mSbjctToken,
cd.mSbjctStrand,
rank,
cd.frame,
cd.mPeptideFrom,
cd.mPeptideTo,
cd.mGenomeFrom,
cd.mGenomeTo))) + "\n")
elif options.format == "cdnas":
print string.join(map(str, (entry.mPredictionId,
entry.mQueryToken,
entry.mSbjctToken,
entry.mSbjctStrand,
entry.mSbjctGenomeFrom - offset,
entry.mSbjctGenomeTo - offset,
genomic_sequence)), "\t")
elif options.format == "map":
map_prediction2genome = alignlib_lite.makeAlignmentSet()
for cd in cds:
alignlib_lite.addDiagonal2Alignment(map_prediction2genome,
cd.mPeptideFrom + 1,
cd.mPeptideTo,
(cd.mGenomeFrom - offset) - cd.mPeptideFrom)
print string.join(map(str, (entry.mPredictionId,
entry.mSbjctToken,
entry.mSbjctStrand,
alignlib_lite.AlignmentFormatEmissions(map_prediction2genome))), "\t")
elif options.format == "intron-fasta":
rank = 0
if len(cds) == 1:
nskipped += 1
continue
last = cds[0].mGenomeTo
for cd in cds[1:]:
rank += 1
key = "%s %i %s:%s:%i:%i" % (
entry.mPredictionId, rank, entry.mSbjctToken, entry.mSbjctStrand, last, entry.mSbjctGenomeFrom)
sequence = genomic_sequence[
last - entry.mSbjctGenomeFrom:cd.mGenomeFrom - entry.mSbjctGenomeFrom]
options.stdout.write(">%s\n%s\n" % (key, sequence))
last = cd.mGenomeTo
elif options.format == "gff-match":
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tTarget \"%s\" %i %i; Score %i; Introns %i; Frameshifts %i; Stops %i" % \
(entry.mSbjctToken,
"gpipe", "similarity",
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo,
entry.mPercentIdentity,
entry.mSbjctStrand,
".",
entry.mQueryToken,
entry.mQueryFrom,
entry.mQueryTo,
entry.score,
entry.mNIntrons,
entry.mNFrameShifts,
entry.mNStopCodons)
elif options.format == "gff-exon":
rank = 0
for cd in cds:
rank += 1
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tTarget \"%s\" %i %i; Score %i; Rank %i/%i; Prediction %i" % \
(entry.mSbjctToken,
"gpipe", "similarity",
cd.mGenomeFrom,
cd.mGenomeTo,
entry.mPercentIdentity,
entry.mSbjctStrand,
".",
entry.mQueryToken,
cd.mPeptideFrom / 3 + 1,
cd.mPeptideTo / 3 + 1,
entry.score,
rank,
len(cds),
entry.mPredictionId)
else:
exon_from = 0
for cd in cds:
cd.mPeptideFrom = exon_from
exon_from += cd.mGenomeTo - cd.mGenomeFrom
cd.mPeptideTo = exon_from
print string.join(map(str, (cds_id, entry.mPredictionId,
cd.mPeptideFrom, cd.mPeptideTo,
cd.frame,
cd.mGenomeFrom, cd.mGenomeTo,
cd.mSequence
)), "\t")
cds_id += 1
noutput += 1
print E.GetParams()
last_exon = Exons.Exon()
contig_sizes = {}
if param_filename_contigs:
infile = open(param_filename_contigs, "r")
for line in infile:
if line[0] == "#":
continue
sbjct_token, size = line[:-1].split("\t")[:2]
contig_sizes[sbjct_token] = int(size)
map_prediction2genome = alignlib_lite.makeAlignmentSet()
nexons, npairs = 0, 0
for line in sys.stdin:
if line[0] == "#":
continue
this_exon = Exons.Exon()
this_exon.Read(line)
if this_exon.mSbjctStrand == "-":
this_exon.InvertGenomicCoordinates(
contig_sizes[this_exon.mSbjctToken])
nexons += 1
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: gpipe/predictions2cds.py 1858 2008-05-13 15:07:05Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome.")
parser.add_option("-o",
"--forward-coordinates",
dest="forward_coordinates",
action="store_true",
help="input uses forward coordinates.")
parser.add_option("-f",
"--format",
dest="format",
type="choice",
choices=("default", "cds", "cdnas", "map", "gff",
"intron-fasta", "exons"),
help="output format.")
parser.add_option("-r",
"--reset-to-start",
dest="reset_to_start",
action="store_true",
help="move genomic coordinates to begin from 0.")
parser.add_option("--reset-query",
dest="reset_query",
action="store_true",
help="move peptide coordinates to begin from 0.")
parser.set_defaults(genome_file=None,
forward_coordinates=False,
format="default",
reset_to_start=False,
reset_query=False)
(options, args) = E.Start(parser, add_pipe_options=True)
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
cds_id = 1
entry = PredictionParser.PredictionParserEntry()
fasta = IndexedFasta.IndexedFasta(options.genome_file)
ninput, noutput, nskipped, nerrors = 0, 0, 0, 0
for line in sys.stdin:
if line[0] == "#":
continue
if line.startswith("id"):
continue
ninput += 1
try:
entry.Read(line)
except ValueError, msg:
options.stdlog.write("# parsing failed with msg %s in line %s" %
(msg, line))
nerrors += 1
continue
cds = Exons.Alignment2Exons(entry.mMapPeptide2Genome,
query_from=entry.mQueryFrom,
sbjct_from=entry.mSbjctGenomeFrom,
add_stop_codon=0)
for cd in cds:
cd.mSbjctToken = entry.mSbjctToken
cd.mSbjctStrand = entry.mSbjctStrand
if cds[-1].mGenomeTo != entry.mSbjctGenomeTo:
options.stdlog.write(
"# WARNING: discrepancy in exon calculation!!!\n")
for cd in cds:
options.stdlog.write("# %s\n" % str(cd))
options.stdlog.write("# %s\n" % entry)
lsequence = fasta.getLength(entry.mSbjctToken)
genomic_sequence = fasta.getSequence(entry.mSbjctToken,
entry.mSbjctStrand,
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo)
# deal with forward coordinates: convert them to negative strand
# coordinates
if options.forward_coordinates and \
entry.mSbjctStrand == "-":
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo = lsequence - \
entry.mSbjctGenomeTo, lsequence - entry.mSbjctGenomeFrom
for cd in cds:
cd.InvertGenomicCoordinates(lsequence)
# attach sequence to cds
for cd in cds:
start = cd.mGenomeFrom - entry.mSbjctGenomeFrom
end = cd.mGenomeTo - entry.mSbjctGenomeFrom
cd.mSequence = genomic_sequence[start:end]
# reset coordinates for query
if options.reset_to_start:
offset = entry.mPeptideFrom
for cd in cds:
cd.mPeptideFrom -= offset
cd.mPeptideTo -= offset
# play with coordinates
if options.reset_to_start:
offset = entry.mSbjctGenomeFrom
for cd in cds:
cd.mGenomeFrom -= offset
cd.mGenomeTo -= offset
else:
offset = 0
if options.format == "cds":
rank = 0
for cd in cds:
rank += 1
cd.mQueryToken = entry.mQueryToken
cd.mSbjctToken = entry.mSbjctToken
cd.mSbjctStrand = entry.mSbjctStrand
cd.mRank = rank
print str(cd)
if options.format == "exons":
rank = 0
for cd in cds:
rank += 1
options.stdout.write("\t".join(
map(str, (entry.mPredictionId, cd.mSbjctToken,
cd.mSbjctStrand, rank, cd.frame, cd.mPeptideFrom,
cd.mPeptideTo, cd.mGenomeFrom, cd.mGenomeTo))) +
"\n")
elif options.format == "cdnas":
print string.join(
map(str,
(entry.mPredictionId, entry.mQueryToken, entry.mSbjctToken,
entry.mSbjctStrand, entry.mSbjctGenomeFrom - offset,
entry.mSbjctGenomeTo - offset, genomic_sequence)), "\t")
elif options.format == "map":
map_prediction2genome = alignlib_lite.makeAlignmentSet()
for cd in cds:
alignlib_lite.addDiagonal2Alignment(
map_prediction2genome, cd.mPeptideFrom + 1, cd.mPeptideTo,
(cd.mGenomeFrom - offset) - cd.mPeptideFrom)
print string.join(
map(str, (entry.mPredictionId, entry.mSbjctToken,
entry.mSbjctStrand,
alignlib_lite.AlignmentFormatEmissions(
map_prediction2genome))), "\t")
elif options.format == "intron-fasta":
rank = 0
if len(cds) == 1:
nskipped += 1
continue
last = cds[0].mGenomeTo
for cd in cds[1:]:
rank += 1
key = "%s %i %s:%s:%i:%i" % (
entry.mPredictionId, rank, entry.mSbjctToken,
entry.mSbjctStrand, last, entry.mSbjctGenomeFrom)
sequence = genomic_sequence[last - entry.mSbjctGenomeFrom:cd.
mGenomeFrom -
entry.mSbjctGenomeFrom]
options.stdout.write(">%s\n%s\n" % (key, sequence))
last = cd.mGenomeTo
elif options.format == "gff-match":
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tTarget \"%s\" %i %i; Score %i; Introns %i; Frameshifts %i; Stops %i" % \
(entry.mSbjctToken,
"gpipe", "similarity",
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo,
entry.mPercentIdentity,
entry.mSbjctStrand,
".",
entry.mQueryToken,
entry.mQueryFrom,
entry.mQueryTo,
entry.score,
entry.mNIntrons,
entry.mNFrameShifts,
entry.mNStopCodons)
elif options.format == "gff-exon":
rank = 0
for cd in cds:
rank += 1
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tTarget \"%s\" %i %i; Score %i; Rank %i/%i; Prediction %i" % \
(entry.mSbjctToken,
"gpipe", "similarity",
cd.mGenomeFrom,
cd.mGenomeTo,
entry.mPercentIdentity,
entry.mSbjctStrand,
".",
entry.mQueryToken,
cd.mPeptideFrom / 3 + 1,
cd.mPeptideTo / 3 + 1,
entry.score,
rank,
len(cds),
entry.mPredictionId)
else:
exon_from = 0
for cd in cds:
cd.mPeptideFrom = exon_from
exon_from += cd.mGenomeTo - cd.mGenomeFrom
cd.mPeptideTo = exon_from
print string.join(
map(str, (cds_id, entry.mPredictionId, cd.mPeptideFrom,
cd.mPeptideTo, cd.frame, cd.mGenomeFrom,
cd.mGenomeTo, cd.mSequence)), "\t")
cds_id += 1
noutput += 1
