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/patch_translations.py 1841 2008-05-08 12:07:13Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome.")
parser.set_defaults(genome_file=None, )
(options, args) = E.Start(parser, add_pipe_options=True)
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
entry = PredictionParser.PredictionParserEntry()
fasta = IndexedFasta.IndexedFasta(options.genome_file)
ninput, noutput = 0, 0
for line in sys.stdin:
if line[0] == "#":
print line[:-1]
continue
entry.Read(line)
ninput += 1
# get genomic sequence
genomic_sequence = fasta.getSequence(entry.mSbjctToken,
entry.mSbjctStrand,
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo)
entry.mMapPeptide2Translation, entry.mTranslation = Genomics.Alignment2PeptideAlignment(
entry.mMapPeptide2Genome, entry.mQueryFrom, 0, genomic_sequence)
options.stdout.write(str(entry) + "\n")
noutput += 1
if options.loglevel >= 1:
options.stdlog.write("# ninput=%i, noutput=%i\n" % (ninput, noutput))
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
parser = E.OptionParser(
version=
"%prog version: $Id: gpipe/gff2predictions.py 2021 2008-07-10 16:00:48Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-t",
"--trans",
dest="trans",
help="input is translated DNA.",
action="store_true")
parser.add_option("-f",
"--format",
dest="format",
help="input format.",
type="choice",
choices=("exons", "psl", "gff"))
parser.add_option("-o",
"--output-format",
dest="output_format",
help="output format",
type="choice",
choices=('exontable', 'exons', 'predictions', 'cds',
'fasta'))
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genomic data (indexed).")
parser.add_option(
"--predictions-file",
dest="predictions_file",
type="string",
help=
"filename with predictions. Use gene structures from this file if available."
)
parser.add_option("-i",
"--gff-field-id",
dest="gff_field_id",
type="string",
help="field for the feature id in the gff info section.")
parser.add_option(
"-p",
"--filename-peptides",
dest="filename_peptides",
type="string",
help=
"Filename with peptide sequences. If given, it is used to check the predicted translated sequences."
)
parser.add_option(
"--no-realignment",
dest="do_realignment",
action="store_false",
help="do not re-align entries that do not parse correctly.")
parser.add_option(
"--remove-unaligned",
dest="remove_unaligned",
action="store_true",
help="remove entries that have not been aligned correctly.")
parser.add_option(
"--input-coordinates",
dest="input_coordinates",
type="string",
help=
"specify input format for input coordinates [forward|both-zero|one-closed|open]."
)
parser.set_defaults(trans=False,
output_format="predictions",
format="psl",
gff_field_id='id',
input_coordinates="both-zero-open",
filename_peptides=None,
genome_file=None,
do_realignment=True,
predictions_file=None,
remove_unaligned=False)
(options, args) = E.Start(parser)
if not options.genome_file:
raise "please specify a genome file."
fasta = IndexedFasta.IndexedFasta(options.genome_file)
contig_sizes = fasta.getContigSizes()
ninput, noutput, nskipped = 0, 0, 0
nfound, nnotfound, nidentical, nmismatch, naligned, nunaligned = 0, 0, 0, 0, 0, 0
if options.filename_peptides:
peptide_sequences = Genomics.ReadPeptideSequences(
IOTools.openFile(options.filename_peptides, "r"))
predictor = Predictor.PredictorExonerate()
predictor.mLogLevel = 0
else:
peptide_sequences = None
predictor = None
converter = IndexedFasta.getConverter(options.input_coordinates)
predictions = {}
if options.predictions_file:
parser = PredictionParser.iterator_predictions(
IOTools.openFile(options.predictions_file, "r"))
for p in parser:
predictions[p.mPredictionId] = p
if options.output_format == "predictions":
if options.format == "psl":
if options.trans:
parser = PredictionParser.PredictionParserBlatTrans()
else:
parser = PredictionParser.PredictionParserBlatCDNA()
nmatches = 1
for line in sys.stdin:
if line[0] == "#":
continue
if not re.match("^[0-9]", line):
continue
try:
entries = parser.Parse((line, ))
except PredictionParser.AlignmentError, e:
print "# %s" % str(e)
print "#", line[:-1]
sys.exit(1)
for entry in entries:
entry.mPredictionId = nmatches
nmatches += 1
print str(entries)
elif options.format == "exons":
parser = PredictionParser.PredictionParserExons(
contig_sizes=contig_sizes)
else:
raise "unknown format %s for output option %s" % (
options.format, options.output_format)
if options.loglevel >= 2:
options.stdlog.write("# parsing.\n")
options.stdlog.flush()
results = parser.Parse(sys.stdin.readlines())
if options.loglevel >= 2:
options.stdlog.write("# parsing finished.\n")
options.stdlog.flush()
if options.loglevel >= 1:
options.stdlog.write(
"# parsing: ninput=%i, noutput=%i, nerrors=%i\n" %
(parser.GetNumInput(), parser.GetNumOutput(),
parser.GetNumErrors()))
for error, msg in parser.mErrors:
options.stdlog.write("# %s : %s\n" % (str(error), msg))
options.stdlog.flush()
# if genomes are given: build translation
if options.genome_file:
results.Sort(lambda x, y: cmp(x.mSbjctToken, y.mSbjctToken))
new_results = PredictionParser.Predictions()
for entry in results:
ninput += 1
if options.loglevel >= 2:
options.stdlog.write(
"# processing entry %s:%s on %s:%s %i/%i.\n" %
(entry.mPredictionId, entry.mQueryToken,
entry.mSbjctToken, entry.mSbjctStrand, ninput,
len(results)))
options.stdlog.flush()
try:
lgenome = fasta.getLength(entry.mSbjctToken)
# added 3 residues - was a problem at split codons just before the stop.
# See for example the chicken sequence ENSGALP00000002741
genomic_sequence = fasta.getSequence(
entry.mSbjctToken, entry.mSbjctStrand,
entry.mSbjctGenomeFrom,
min(entry.mSbjctGenomeTo + 3, lgenome))
except KeyError:
if options.loglevel >= 1:
options.stdlog.write(
"# did not find entry for %s on %s.\n" %
(entry.mPredictionId, entry.mSbjctToken))
nskipped += 1
continue
if predictions and entry.mPredictionId in predictions:
if options.loglevel >= 2:
options.stdlog.write(
"# substituting entry %s on %s:%s.\n" %
(entry.mPredictionId, entry.mSbjctToken,
entry.mSbjctStrand))
options.stdlog.flush()
entry = predictions[entry.mPredictionId]
exons = Exons.Alignment2Exons(entry.mMapPeptide2Genome, 0,
entry.mSbjctGenomeFrom)
entry.mMapPeptide2Translation, entry.mTranslation = Genomics.Alignment2PeptideAlignment(
Genomics.String2Alignment(entry.mAlignmentString),
entry.mQueryFrom, 0, genomic_sequence)
entry.score = entry.mMapPeptide2Translation.getColTo(
) - entry.mMapPeptide2Translation.getColFrom() + 1
(entry.mNIntrons, entry.mNFrameShifts, entry.mNGaps, entry.mNSplits, entry.mNStopCodons, entry.mNDisruptions ) = \
Genomics.CountGeneFeatures(0,
entry.mMapPeptide2Genome,
genomic_sequence)
if peptide_sequences:
if str(entry.mPredictionId) in peptide_sequences:
reference = peptide_sequences[str(
entry.mPredictionId)].upper()
translation = entry.mTranslation
nfound += 1
is_identical, nmismatches = checkIdentity(
reference, translation, options)
if is_identical:
nidentical += 1
else:
nmismatch += 1
if options.do_realignment:
if options.loglevel >= 2:
options.stdlog.write(
"# %s: mismatches..realigning in region %i:%i\n"
% (entry.mPredictionId,
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo))
options.stdlog.flush()
result = predictor(
entry.mPredictionId, reference,
entry.mSbjctToken, genomic_sequence,
"--subopt FALSE --score '%s'" %
str(80))
# "--exhaustive --subopt FALSE --score '%s'" % str(80) )
if result:
translation = result[0].mTranslation
is_identical, nmismatches = checkIdentity(
reference, translation, options)
else:
if options.loglevel >= 2:
options.stdlog.write(
"# %s: realignment returned empty result\n"
% (entry.mPredictionId))
options.stdlog.flush()
is_identical = False
if is_identical:
naligned += 1
prediction_id = entry.mPredictionId
sbjct_genome_from = entry.mSbjctGenomeFrom
entry = result[0]
entry.mPredictionId = prediction_id
entry.mSbjctGenomeFrom += sbjct_genome_from
else:
nunaligned += 1
if options.loglevel >= 1:
options.stdlog.write(
"# %s: mismatch on %s:%s:%i-%i after realignment\n# reference =%s\n# translated=%s\n# realigned =%s\n"
%
(entry.mPredictionId,
entry.mSbjctToken,
entry.mSbjctStrand,
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo,
reference, entry.mTranslation,
translation))
options.stdlog.flush()
if options.remove_unaligned:
nskipped += 1
continue
else:
if options.loglevel >= 2:
options.stdlog.write(
"# %s: mismatches on %s ... no realignment\n"
% (
entry.mPredictionId,
entry.mSbjctToken,
))
if options.loglevel >= 3:
options.stdlog.write(
"# %s: mismatch before realignment\n# reference =%s\n# translated=%s\n"
% (entry.mPredictionId, reference,
translation))
options.stdlog.flush()
if options.remove_unaligned:
nskipped += 1
continue
else:
nnotfound += 1
new_results.append(entry)
noutput += 1
results = new_results
if results:
options.stdout.write(str(results) + "\n")
def setTranslation(self, genomic_sequence):
"""set translation from genomic sequence."""
self.mMapPeptide2Translation, self.mTranslation = Genomics.Alignment2PeptideAlignment(
self.mMapPeptide2Genome, self.mQueryFrom, self.mSbjctGenomeFrom,
genomic_sequence)
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser.add_option("-m", "--filename-map", dest="filename_map", type="string",
help="filename with mapping information.")
parser.add_option("-o", "--pattern-old", dest="pattern_old", type="string",
help="pattern for mapping new to old identifiers: extract string from old.")
parser.add_option("-n", "--pattern-new", dest="pattern_new", type="string",
help="pattern for mapping new to old identifiers: put string into new.")
parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
help="genome_file.")
parser.add_option("-p", "--peptides", dest="filename_peptides", type = "string",
help="filename with peptide sequences.")
parser.add_option("-f", "--input-format", dest="input_format", type="choice",
help="format of mapping file", choices=("alignment", "offsets") )
parser.add_option("-i", "--write-missed", dest="write_missed", type="string",
help="write missed identifiers to separate file.")
parser.add_option("-a", "--filename-genes", dest="filename_genes", type="string",
help="filename with gene information.")
parser.add_option("--filename-old-peptides", dest="filename_old_peptides", type="string",
help="filename with old peptide information.")
parser.add_option("--no-renumber", dest="renumber", action="store_false",
help="do not renumber predictions.")
parser.add_option("--contig-sizes-old", dest="contig_sizes_old", type="string",
help="contig sizes for old data.")
parser.add_option("--contig-sizes-new", dest="contig_sizes_new", type="string",
help="contig sizes for new data.")
parser.add_option("--skip-errors", dest="skip_errors", action="store_true",
help="skip entries with errors.")
parser.set_defaults(
filename_map = None,
pattern_old = "(.+)",
pattern_new = "%s",
genome_file = None,
filename_peptides = None,
write_missed = None,
filename_genes = None,
filename_old_peptides = None,
renumber = True,
input_format = "alignment",
contig_sizes_old = None,
contig_sizes_new = None,
skip_errors = None
)
(options, args) = E.Start( parser, add_pipe_options = True)
predictor = PredictorExonerate()
## the different mapping criteria
map_sbjcts = {}
breakpoints = {}
################################################################################################
map_transcript2gene = {}
if options.filename_genes:
infile = open(options.filename_genes, "r")
for gene, transcript in map( lambda x: x[:-1].split("\t")[:2], filter( lambda x: x[0] != "#", infile.readlines())):
map_transcript2gene[transcript] = gene
infile.close()
################################################################################################
peptides = {}
if options.filename_peptides:
peptides = Genomics.ReadPeptideSequences( open(options.filename_peptides, "r"))
options.stdlog.write( "# read %i peptide sequences.\n" % len(peptides))
################################################################################################
## read old query sequences and compare against new query sequences
## this can be used to build a map between old and new queries
query_map_old2new = {}
if options.filename_old_peptides:
old_peptides = Genomics.ReadPeptideSequences( open(options.filename_old_peptides, "r"))
options.stdlog.write( "# read %i old peptide sequences.\n" % len(old_peptides))
query_map_old2new, unmappable, unmapped = Genomics.MapSequences( old_peptides, peptides)
options.stdlog.write( "# built map: unmappable=%i unmapped=%i.\n" % (len(unmappable), len(unmapped)))
if options.loglevel >= 2:
options.stdlog.write( "# unmappable: %s.\n" % ";".join(unmappable))
options.stdlog.write( "# unmapped: %s.\n" % ";".join(unmapped))
################################################################################################
## read old/new contig sizes for mapping positive/negative coordinates
contig_sizes_old = {}
contig_sizes_new = {}
if options.contig_sizes_old:
contig_sizes_old = Genomics.ReadContigSizes( open(options.contig_sizes_old, "r") )
if options.contig_sizes_new:
contig_sizes_new = Genomics.ReadContigSizes( open(options.contig_sizes_new, "r") )
################################################################################################
if options.filename_map:
infile = open(options.filename_map)
if options.input_format == "alignments":
for line in infile:
if line[0] == "#": continue
x, old_token, old_from, old_to, old_ali, new_from, new_to, new_ali = line[:-1].split("\t")
map_sbjcts[old_token] = (old_from, old_ali, new_from, new_ali)
if options.loglevel >= 1:
options.stdlog.write( "# read %i alignments.\n" % len(map_sbjcts))
elif options.input_format == "offsets":
## input is a list of segments and their offsets.
breakpoints, endpoints, offsets = ReadOffsets( infile )
if options.loglevel >= 1:
options.stdlog.write( "# read breakpoints for %i chromosomes.\n" % len(breakpoints))
infile.close()
################################################################################################
################################################################################################
################################################################################################
## end of input section
################################################################################################
################################################################################################
################################################################################################
rx = re.compile(options.pattern_old)
last_sbjct_token = None
ninput = 0
nerrors = 0
nerrors_map = 0
nerrors_inconsistencies = 0
nerrors_boundaries = 0
nerrors_translation = 0
nerrors_inconsequential = 0
nerrors_realigned = 0
nmapped = 0
nfiltered = 0
naligned = 0
noutput = 0
found_transcripts = {}
nduplicates = 0
output = {}
for line in sys.stdin:
if line[0] == "#": continue
entry = PredictionParser.PredictionParserEntry()
entry.Read( line )
ninput += 1
is_positive = entry.mSbjctStrand == "+"
is_error = False
## check if query token is mappable: using sequence map
if (query_map_old2new and entry.mQueryToken not in query_map_old2new):
options.stdlog.write("# skipping prediction %i: obsolete query %s\n" % (entry.mPredictionId, entry.mQueryToken) )
nfiltered += 1
continue
else:
## check if query token is mappable: using filter
if (peptides and entry.mQueryToken not in peptides):
options.stdlog.write("# skipping prediction %i: obsolete query %s\n" % (entry.mPredictionId, entry.mQueryToken) )
nfiltered += 1
continue
new_sbjct_token = options.pattern_new % rx.search(entry.mSbjctToken).groups()[0]
##########################################################################################################
## Map via alignments
if entry.mSbjctToken in map_sbjcts:
nmapped += 1
if last_sbjct_token != entry.mSbjctToken:
old_from, old_ali, new_from, new_ali = map_sbjcts[entry.mSbjctToken]
map_a2b = alignlib_lite.makeAlignmentVector()
alignlib_lite.AlignmentFormatExplicit(
int(old_from), old_ali,
int(new_from), new_ali).copy( map_a2b )
last_sbjct_token = entry.mSbjctToken
if options.loglevel >= 3:
print "#", str(entry)
print "#", map_sbjcts[entry.mSbjctToken]
sys.stdout.flush()
old_f, old_t = entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo
## convert to forward coordinates:
if is_positive:
f, t= old_f, old_t
first_res, last_res = f + 1, t
else:
f, t = map_a2b.getRowTo() - old_f, map_a2b.getRowTo() - old_t
first_res, last_res = f, t + 1
## map first and last residues
mfirst_res = map_a2b.mapRowToCol( first_res )
mlast_res = map_a2b.mapRowToCol( last_res )
if (mfirst_res == 0 and old_f != 0) or (mlast_res == 0 and old_t != map_a2b.getRowTo() ):
options.stderr.write("# mapping not possible for prediction %i on %s %s:%i-%i -> %i-%i -> %i-%i -> %i-%i -> %i-%i\n" % \
(entry.mPredictionId, entry.mSbjctToken, entry.mSbjctStrand,
old_f, old_t,
f, t,
first_res, last_res,
mfirst_res, mlast_res,
f, t))
options.stderr.write("# %s\n" % str(map_sbjcts[entry.mSbjctToken]))
options.stderr.write("# %s\n" % str(entry))
options.stderr.flush()
nerrors_boundaries += 1
is_error = True
## get extended boundaries for alignment later on
while mfirst_res == 0 and first_res > 1:
first_res -= 1
mfirst_res = map_a2b.mapRowToCol(first_res)
while mlast_res == 0 and last_res < map_a2b.getRowTo():
last_res += 1
mlast_res = map_a2b.mapRowToCol(last_res)
## convert to genomic coordinates
## convert negative strand coordinates
if is_positive:
new_f = mfirst_res - 1
new_t = mlast_res
else:
new_f = mfirst_res
new_t = mlast_res - 1
new_f = map_a2b.getColTo() - new_f
new_t = map_a2b.getColTo() - new_t
## Now map the alignment.
try:
MapAlignment( entry, map_a2b )
except ValueError:
options.stderr.write("# alignment mapping not possible for prediction %i on %s %s:%i-%i -> %i-%i -> %i-%i -> %i-%i -> %i-%i -> %i-%i\n" % \
(entry.mPredictionId, entry.mSbjctToken, entry.mSbjctStrand,
old_f, old_t,
f, t,
first_res, last_res,
mfirst_res, mlast_res,
new_f, new_t,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo))
options.stderr.write("# %s\n" % str(map_sbjcts[entry.mSbjctToken]))
options.stderr.flush()
nerrors_map += 1
is_error= True
if new_f != entry.mSbjctGenomeFrom or new_t != entry.mSbjctGenomeTo:
options.stderr.write("# mapping inconsistency for prediction %i on %s %s:%i-%i -> %i-%i -> %i-%i -> %i-%i -> %i-%i <> %i-%i\n" % \
(entry.mPredictionId, entry.mSbjctToken, entry.mSbjctStrand,
old_f, old_t,
f, t,
first_res, last_res,
mfirst_res, mlast_res,
new_f, new_t,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo))
nerrors_inconsistencies += 1
is_error = True
##########################################################################################################
## Map via offsets
if entry.mSbjctToken in breakpoints:
old_f, old_t = entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo
## convert to forward coordinates:
if is_positive:
f, t= old_f, old_t
else:
f, t = contig_sizes_old[entry.mSbjctToken] - old_t, contig_sizes_old[entry.mSbjctToken] - old_f
o1 = GetOffset( f,
breakpoints[entry.mSbjctToken],
endpoints[entry.mSbjctToken],
offsets[entry.mSbjctToken] )
o2 = GetOffset( t,
breakpoints[entry.mSbjctToken],
endpoints[entry.mSbjctToken],
offsets[entry.mSbjctToken] )
if o1 != o2:
options.stderr.write("# break within gene %s\n" % str(entry))
nerrors_map += 1
is_error = True
f += o1
t += o2
if not is_positive:
f, t = contig_sizes_new[entry.mSbjctToken] - t, contig_sizes_new[entry.mSbjctToken] - f
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo = f, t
if entry.mSbjctGenomeFrom > entry.mSbjctGenomeTo:
options.stderr.write("# mapping error: start after end %s\n" % str(entry))
nerrors_map += 1
is_error = True
##########################################################################################################
## do translation check, if genome is given
if options.genome_file:
genomic_sequence = Genomics.GetGenomicSequence( new_sbjct_token, entry.mSbjctStrand,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo,
options.genome_file,
loglevel = 0)
map_peptide2translation, translation = Genomics.Alignment2PeptideAlignment( \
entry.mMapPeptide2Genome, entry.mQueryFrom, 0, genomic_sequence )
if re.sub("X", "", translation) != re.sub("X", "", entry.mTranslation):
options.stderr.write("# translation error for prediction %i on %s %s:%i-%i -> %i-%i <> %i-%i\n" % \
(entry.mPredictionId, entry.mSbjctToken, entry.mSbjctStrand,
old_f, old_t,
f, t,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo))
if map_sbjcts:
options.stderr.write("# %s\n" % str(map_sbjcts[entry.mSbjctToken]))
options.stderr.write("# old=%s\n# new=%s\n" % (entry.mTranslation, translation))
options.stderr.write("# old=%s\n# new=%s\n" % (entry.mAlignmentString, Genomics.Alignment2String(entry.mMapPeptide2Genome)))
nerrors_translation += 1
is_error = True
if peptides and entry.mQueryToken in peptides:
naligned += 1
options.stdlog.write( "# aligning: %s versus %s:%s: %i-%i\n" % ( \
entry.mQueryToken,
new_sbjct_token, entry.mSbjctStrand,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo))
# do a quick reprediction
if entry.mQueryToken in peptides:
genomic_sequence = Genomics.GetGenomicSequence( new_sbjct_token, entry.mSbjctStrand,
0, 0,
genome_file = options.genome_pattern,
loglevel = 0)
predictor.mLogLevel = 0
result = predictor(entry.mQueryToken, peptides[entry.mQueryToken],
entry.mSbjctToken, genomic_sequence,
"--exhaustive --subopt FALSE --score '%s' " % str(80),
new_f - 10, new_t + 10)
prediction_id = entry.mPredictionId
if result:
entry = result[0]
entry.mPredictionId = prediction_id
nerrors_realigned += 1
else:
if is_error:
nerrors_inconsequential += 1
entry.mSbjctToken = new_sbjct_token
## map query tokens
if query_map_old2new:
query_tokens = query_map_old2new[entry.mQueryToken]
else:
query_tokens = (entry.mQueryToken,)
if options.skip_errors and is_error:
continue
for query_token in query_tokens:
entry.mQueryToken = query_token
prediction_id = entry.mPredictionId
entry.mPredictionId = 0
hid = Genomics.GetHID( str(entry) )
if hid in output:
nduplicates += 1
continue
noutput += 1
if options.renumber: prediction_id = noutput
entry.mPredictionId = prediction_id
options.stdout.write( str(entry) + "\n")
options.stdout.flush()
found_transcripts[entry.mQueryToken] = 1
## write out found transcripts and genes
nmissed_transcripts = 0
missed_transcripts = []
found_genes = {}
if peptides:
for x in peptides.keys():
if x not in found_transcripts:
nmissed_transcripts += 1
missed_transcripts.append( x )
else:
found_genes[map_transcript2gene[x]] = 1
missed_genes = {}
nmissed_genes = 0
if map_transcript2gene:
for t in missed_transcripts:
g = map_transcript2gene[t]
if g not in found_genes:
missed_genes[g] = 1
nmissed_genes = len(missed_genes)
if options.write_missed:
outfile = open(options.write_missed, "w")
for x in missed_transcripts:
if x in unmapped:
status = "unmapped"
else:
status = "mapped"
outfile.write( "%s\t%s\t%s\n" % ("transcript", x, status ))
for x in missed_genes:
status = "unknown"
outfile.write( "%s\t%s\t%s\n" % ("gene", x, status ))
outfile.close()
options.stdlog.write("# input=%i, output=%i, filtered=%i, nduplicates=%i, mapped=%i, errors=%i\n" % (\
ninput, noutput, nfiltered, nduplicates, nmapped, nerrors ))
options.stdlog.write("# errors: inconsequental=%i, boundaries=%i, mapping=%i, inconsistencies=%i, translation=%i, realigned=%i\n" % (\
nerrors_inconsequential, nerrors_boundaries, nerrors_map, nerrors_inconsistencies, nerrors_translation, nerrors_realigned ))
options.stdlog.write("# peptides: input=%i, found=%i, missed=%i, found_genes=%i, missed_genes=%i\n" % (\
len(peptides), len(found_transcripts), nmissed_transcripts, len(found_genes), nmissed_genes) )
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
parser = E.OptionParser(
version=
"%prog version: $Id: mali2predictions.py 2781 2009-09-10 11:33:14Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome.")
parser.add_option("-l",
"--filename-locations",
dest="filename_locations",
type="string",
help="filename with locations")
parser.add_option("-m",
"--master",
dest="master",
type="string",
help="the master determines the frame.")
parser.set_defaults(filename_locations=None, gap_chars="-.", master=None)
(options, args) = E.Start(parser, add_pipe_options=True)
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
mali = Mali.Mali()
mali.readFromFile(sys.stdin)
identifiers = mali.getIdentifiers()
aligned_columns, aligned_exons = getAlignedColumns(mali, options)
map_id2location = {}
if options.filename_locations:
map_id2location = IOTools.ReadMap(open(options.filename_locations,
"r"))
options.stdout.write(Prediction.Prediction().getHeader() + "\n")
nid = 1
for identifier in identifiers:
if options.loglevel >= 2:
options.stdlog.write("# processing %s\n" % (identifier))
entry = mali.getEntry(identifier)
sequence = entry.mString
if sequence[0] not in string.lowercase:
raise "all sequences should start with an exon."
was_exon = True
d = 0
alignment = []
carry_over = 0
last_codon = []
codon = []
nchars_in_codon = 0
n = 0
last_master_residue = 0
master_residue = 0
for column in range(len(sequence)):
c = sequence[column]
is_gap = c in options.gap_chars
is_aligned = column in aligned_columns
is_exon = column in aligned_exons
if is_gap:
continue
if is_exon:
master_residue = aligned_exons[column]
codon.append((n, master_residue))
n += 1
# check if we have a complete codon
if is_exon:
# A codon is complete, if it ends at frame 2 or
# it spans more than one codons in the master.
# Gaps in the master that are a multiple of 3 are ignored
d = master_residue - last_master_residue - 1
if master_residue % 3 == 2 or (d % 3 != 0 and d > 0):
if last_codon:
d = codon[0][0] - last_codon[-1][0] - 1
if d > 0:
# add in-frame introns
if d > 10:
alignment.append(["5", 0, 2])
alignment.append(["I", 0, d - 4])
alignment.append(["3", 0, 2])
else:
raise "untreated case"
alignment += processCodon(codon)
last_codon = codon
codon = []
last_master_residue = master_residue
last = alignment[0]
new_alignment = []
for this in alignment[1:]:
if this[0] == last[0]:
last[1] += this[1]
last[2] += this[2]
continue
new_alignment.append(last)
last = this
new_alignment.append(last)
if options.loglevel >= 4:
options.stdlog.write("# output=%s\n" % (str(new_alignment)))
assert (new_alignment[-1][2] % 3 == 0)
lalignment = sum(map(lambda x: x[2], new_alignment))
prediction = Prediction.Prediction()
prediction.mQueryToken = identifier
genomic_sequence = re.sub("[%s]" % options.gap_chars, "",
mali[identifier])
prediction.mPredictionId = nid
nid += 1
if identifier in map_id2location:
prediction.mSbjctToken, prediction.mSbjctStrand, sfrom, sto = map_id2location[
identifier].split(":")[:4]
prediction.mSbjctGenomeFrom = int(sfrom) + entry.mFrom
prediction.mSbjctGenomeTo = int(sto)
else:
prediction.mSbjctToken = "unk"
prediction.mSbjctStrand = "+"
prediction.mSbjctGenomeFrom = 0
prediction.mQueryCoverage = 100
prediction.mPercentIdentity = 100
prediction.mPercentSimilarity = 100
prediction.mQueryLength = prediction.mQueryTo
prediction.mSbjctGenomeTo = prediction.mSbjctGenomeFrom + lalignment
prediction.mMapPeptide2Genome = new_alignment
prediction.mAlignmentString = string.join(
map(lambda x: string.join(map(str, x), " "),
prediction.mMapPeptide2Genome), " ")
prediction.mMapPeptide2Translation, prediction.mTranslation = Genomics.Alignment2PeptideAlignment(
prediction.mMapPeptide2Genome, 0, 0, genomic_sequence)
(prediction.mNIntrons, prediction.mNFrameShifts, prediction.mNGaps, prediction.mNSplits, prediction.mNStopCodons, disruptions) = \
Genomics.CountGeneFeatures(0,
prediction.mMapPeptide2Genome,
genomic_sequence)
options.stdout.write(str(prediction) + "\n")
E.Stop()
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser( version = "%prog version: $Id: gpipe/predictions2transcripts.py 1841 2008-05-08 12:07:13Z andreas $",
usage = globals()["__doc__"] )
parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome." )
parser.add_option("-o", "--output-filename-summary", dest="output_filename_summary", type="string",
help="filename with summary information." )
parser.add_option( "--skip-header", dest="skip_header", action="store_true",
help="skip header." )
parser.add_option( "--start-codon-boundary", dest="start_codon_boundary", type="int",
help="maximum extension for start codon (make divisible by 3)." )
parser.add_option( "--stop-codon-boundary", dest="stop_codon_boundary", type="int",
help="maximum extension for stop codon (make divisible by 3)." )
parser.add_option( "--left-extension-mode", dest="left_extension_mode", type="choice",
choices=("first-start", "first-stop-backtrack"),
help="extension mode for 5' end.")
parser.add_option( "--fill-introns", dest="fill_introns", type="int",
help="fill intron if divisible by three and no stop codon up to a maximum length of #." )
parser.add_option( "--introns-max-stops", dest="introns_max_stops", type="int",
help="maximum number of stop codons to tolerate within an intron." )
parser.add_option( "--output-format", dest="output_format", type="choice",
choices=("predictions", "extensions", "filled-introns"),
help="output format." )
parser.set_defaults(
genome_file = "genome",
start_codons = ("ATG"),
stop_codons = ("TAG", "TAA", "TGA"),
start_codon_boundary = 9999,
stop_codon_boundary = 9999,
fill_introns = 0,
introns_max_stops = 0,
left_splice_signals = ("GT",),
right_splice_signals = ("AG",),
output_format="extensions",
left_extension_mode = "first-start",
skip_header = False,
output_filename_summary = None,
)
(options, args) = E.Start( parser, add_pipe_options = True )
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
options.start_codon_boundary = int(options.start_codon_boundary / 3)
options.stop_codon_boundary = int(options.stop_codon_boundary / 3)
fasta = IndexedFasta.IndexedFasta( options.genome_file )
p = PredictionParser.PredictionParserEntry()
ninput, noutput = 0, 0
nfilled = 0
nseqs_filled = 0
nseqs_extended = 0
left_extensions = []
right_extensions = []
filled_introns = []
if not options.skip_header:
if options.output_format == "predictions":
options.stdout.write( Prediction.Prediction().getHeader() + "\n" )
elif options.output_format == "filled-introns":
options.stdout.write("\t".join( ("prediction_id",
"intron",
"peptide_sequence",
"genomic_sequence") ) + "\n" )
if options.output_filename_summary:
outfile_summary = open (options.output_filename_summary, "w" )
outfile_summary.write( "id\ttype\tnumber\tlength\tfrom\tto\tsequence\n" )
else:
outfile_summary = None
for line in options.stdin:
if line[0] == "#": continue
ninput += 1
p.Read(line)
lsequence = fasta.getLength( p.mSbjctToken )
genome_from = max( 0, p.mSbjctGenomeFrom - options.start_codon_boundary)
genome_to = min( lsequence, p.mSbjctGenomeTo + options.stop_codon_boundary)
genomic_sequence = fasta.getSequence( p.mSbjctToken, p.mSbjctStrand,
genome_from,
genome_to ).upper()
########################################################################
########################################################################
########################################################################
## Do extensions
if options.start_codon_boundary or options.stop_codon_boundary:
extension_start = p.mSbjctGenomeFrom - genome_from
extension_stop = genome_to - p.mSbjctGenomeTo
fragment_to = extension_start + p.mSbjctGenomeTo - p.mSbjctGenomeFrom
lfragment = len(genomic_sequence)
########################################################################
########################################################################
########################################################################
## find start codon
start = extension_start
found_start = False
if options.left_extension_mode == "first-start":
found_start, start = findCodonReverse( genomic_sequence,
start,
options.start_codons,
options.stop_codons )
elif options.left_extension_mode == "first-stop-backtrack":
if genomic_sequence[start:start+3] in options.start_codons:
found_start = True
else:
found_start, start = findCodonReverse( genomic_sequence,
start,
options.stop_codons )
if found_start:
E.info("prediction %s: stop found at %i (%i) backtracking ..." % ( p.mPredictionId, start, extension_start - start) )
## bracktrack to first start codon
found_start = False
while start < extension_start:
start += 3
if genomic_sequence[start:start+3] in options.start_codons:
found_start = True
break
else:
start = extension_start
if found_start:
E.info("start codon found at %i (%i)." % ( start, extension_start - start) )
else:
E.info("no start codon found." )
else:
E.info("prediction %s: no stop found ... backtracking to start codon." % ( p.mPredictionId ) )
found_start, start = findCodonReverse( genomic_sequence, start, options.start_codons )
E.info("prediction %s: no start codon found." % ( p.mPredictionId ) )
if found_start:
start += genome_from
else:
start = p.mSbjctGenomeFrom
dstart = p.mSbjctGenomeFrom - start
########################################################################
########################################################################
########################################################################
## find stop codon
## stop points to the beginning of the codon, thus the stop codon will
## not be part of the sequence.
stop = fragment_to
found_stop = 0
while stop < lfragment and \
genomic_sequence[stop:stop+3] not in ("NNN", "XXX"):
if genomic_sequence[stop:stop+3] in options.stop_codons:
found_stop = 1
break
stop += 3
if found_stop:
stop += genome_from
else:
stop = p.mSbjctGenomeTo
dstop = stop - p.mSbjctGenomeTo
########################################################################
########################################################################
########################################################################
## build new prediction
map_peptide2genome = []
if dstart: map_peptide2genome.append( ("G", 0, dstart) )
map_peptide2genome += p.mMapPeptide2Genome
if dstop: map_peptide2genome.append( ("G", 0, dstop) )
E.info("prediction %s: extension: found_start=%i, found_stop=%i, left=%i, right=%i" % ( p.mPredictionId, found_start, found_stop, dstart, dstop ) )
## save results
p.mMapPeptide2Genome = map_peptide2genome
p.mAlignmentString = Genomics.Alignment2String( map_peptide2genome )
p.mSbjctGenomeFrom -= dstart
p.mSbjctGenomeTo += dstop
p.mSbjctFrom += dstart / 3
p.mSbjctTo += dstart / 3 + dstop / 3
if dstart or dstop:
if dstart: left_extensions.append( dstart )
if dstop: right_extensions.append( dstop )
nseqs_extended += 1
## update genomic sequence because borders might have changed.
genomic_sequence = fasta.getSequence( p.mSbjctToken,
p.mSbjctStrand,
p.mSbjctGenomeFrom,
p.mSbjctGenomeTo ).upper()
if options.fill_introns:
has_filled = False
exons = Exons.Alignment2Exons( p.mMapPeptide2Genome,
query_from = 0,
sbjct_from = 0 )
new_exons = []
last_e = exons[0]
nintron = 0
for e in exons[1:]:
nintron += 1
lintron = e.mGenomeFrom - last_e.mGenomeTo
if lintron > options.fill_introns or (lintron) % 3 != 0:
E.debug( "prediction %s: intron %i of size %i discarded." % \
(p.mPredictionId,
nintron, lintron ) )
new_exons.append(last_e)
last_e = e
continue
## get sequence, include also residues from split codons
## when checking for stop codons.
if e.mAlignment[0][0] == "S":
offset_left = last_e.mAlignment[-1][2]
offset_right = e.mAlignment[0][2]
else:
offset_left, offset_right = 0, 0
sequence = genomic_sequence[last_e.mGenomeTo - offset_left:e.mGenomeFrom+offset_right]
## check for splice sites
for signal in options.left_splice_signals:
if sequence[offset_left:offset_left+len(signal)] == signal:
left_signal = True
break
else:
left_signal = False
for signal in options.right_splice_signals:
if sequence[-(len(signal)+offset_right):-offset_right] == signal:
right_signal = True
break
else:
right_signal = False
nstops, ngaps = 0, 0
for codon in [ sequence[x:x+3] for x in range(0,len(sequence),3) ]:
if codon in options.stop_codons: nstops += 1
if "N" in codon.upper(): ngaps += 1
E.debug( "prediction %s: intron %i of size %i (%i-%i) (%s:%s:%i:%i): stops=%i, gaps=%i, signals=%s,%s." % \
(p.mPredictionId,
nintron, lintron,
offset_left, offset_right,
p.mSbjctToken, p.mSbjctStrand,
p.mSbjctGenomeFrom + last_e.mGenomeTo,
p.mSbjctGenomeFrom + e.mGenomeFrom,
nstops,
ngaps,
left_signal, right_signal ) )
if nstops + ngaps > options.introns_max_stops:
new_exons.append(last_e)
last_e = e
continue
E.info( "prediction %s: filling intron %i of size %i: stops=%i, gaps=%i, signals=%s,%s" % \
(p.mPredictionId,
nintron, lintron,
nstops,
ngaps,
left_signal, right_signal))
e.Merge( last_e )
has_filled = True
nfilled += 1
last_e = e
if options.output_format == "filled-introns":
options.stdout.write( "\t".join( map(str, ( p.mPredictionId,
nintron,
Genomics.TranslateDNA2Protein( sequence ),
sequence ) ) ) + "\n" )
filled_introns.append(lintron)
p.mNIntrons -= 1
new_exons.append(last_e)
if has_filled: nseqs_filled += 1
Exons.UpdatePeptideCoordinates( new_exons )
p.mMapPeptide2Genome = Exons.Exons2Alignment( new_exons )
p.mAlignmentString = Genomics.Alignment2String( p.mMapPeptide2Genome )
## build translated sequence
p.mMapPeptide2Translation, p.mTranslation = Genomics.Alignment2PeptideAlignment( \
p.mMapPeptide2Genome, p.mQueryFrom, 0, genomic_sequence )
## output info
if options.output_format == "predictions":
options.stdout.write( str(p) + "\n" )
elif options.output_format == "extensions":
if found_start: found_start = 1
if found_stop: found_stop = 1
options.stdout.write( "\t".join( map(str, ( p.mPredictionId,
found_start, found_stop,
dstart, dstop,
p.mTranslation,
p.mSbjctGenomeFrom, p.mSbjctGenomeTo,
p.mAlignmentString ))) + "\n" )
noutput += 1
options.stdout.flush()
E.info("stats : %s" % "\t".join(Stats.DistributionalParameters().getHeaders() ))
E.info("left : %s" % str(Stats.DistributionalParameters(left_extensions)) )
E.info("right : %s" % str(Stats.DistributionalParameters(right_extensions)) )
E.info("introns: %s" % str(Stats.DistributionalParameters(filled_introns)) )
E.info("ninput=%i, noutput=%i, nextended=%i, nfilled=%i, nexons_filled=%i" % (\
ninput, noutput, nseqs_extended, nseqs_filled, nfilled))
E.Stop()
