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/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.makeAlignmentSet()
for cd in cds:
alignlib.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.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
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.makeAlignmentSet()
for cd in cds:
alignlib.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.AlignmentFormatEmissions( map_prediction2genome ))), "\t")
elif options.format == "intron-fasta":
rank = 0
if len(cds) == 1: