try:
cds_fragment = cds_sequences[p.mQueryToken]
except KeyError:
print "# ERROR: cds not found: query %s." % p.mQueryToken
continue
genomic_fragment = genomic_sequence[
p.mSbjctGenomeFrom:p.mSbjctGenomeTo]
if len(genomic_fragment) == 0:
raise "ERROR: empty fragment %s:%s for line" % (
p.mSbjctGenomeFrom, p.mSbjctGenomeTo), line
map_query2sbjct, genomic_fragment = Genomics.Alignment2CDNA(p.mMapPeptide2Genome,
query_from=p.mQueryFrom -
1,
sbjct_from=0,
genome=genomic_fragment)
# check for errors:
if map_query2sbjct.getRowTo() != p.mQueryTo * 3:
print str(p)
raise "# ERROR: boundary shift in query: %i %i" % (
map_query2sbjct.getRowTo(), p.mQueryTo * 3)
if map_query2sbjct.getColTo() > len(genomic_fragment):
print "# ERROR: length mismatch: genomic fragment (%i) shorter than last aligned residue (%i)" %\
(len(genomic_fragment), map_query2sbjct.getColTo())
print "#", line
print "# cds"
print "#", cds_fragment
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/prediction2pairs.py 2031 2008-07-15 09:19:05Z andreas $", usage = globals()["__doc__"])
parser.add_option( "-g", "--genome-file", dest="genome_file", type="string",
help="filename with genomic data (indexed)." )
parser.add_option( "-c", "--cds", dest="filename_cds", type="string",
help="filename with cds seguences." )
parser.add_option( "-f", "--format", dest="format", type="choice",
choices=("paired_fasta", ),
help="output format, valid options are: paired_fasta: concatenated pairwise alignments in FASTA format" )
parser.set_defaults(
genome_file = "genome",
filename_cds = "cds.fasta",
format = "paired_fasta",
filename_suffix = ".fasta",
filename_prefix = "",
)
(options, args) = E.Start( parser, add_psql_options = True )
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(1)
fasta = IndexedFasta.IndexedFasta( options.genome_file )
## reading CDS sequences
if options.filename_cds:
cds_sequences = Genomics.ReadPeptideSequences( open(options.filename_cds, "r") )
else:
cds_sequences = {}
if options.loglevel >= 1:
options.stdlog.write( "# read %i CDS sequences\n" % len(cds_sequences) )
last_filename_genome = None
p = PredictionParser.PredictionParserEntry()
ninput, noutput, nsanity, n3, nlength = 0, 0, 0, 0, 0
for line in options.stdin:
if line[0] == "#": continue
if line[0] == '"': continue
p.Read(line)
ninput += 1
genomic_fragment = fasta.getSequence( p.mSbjctToken, p.mSbjctStrand,
p.mSbjctGenomeFrom, p.mSbjctGenomeTo )
if len(genomic_fragment) == 0:
raise "ERROR: empty fragment %s:%s for line" % (p.mSbjctGenomeFrom, p.mSbjctGenomeTo), line
try:
cds_fragment = cds_sequences[p.mQueryToken]
except KeyError:
options.stdlog.write( "# ERROR: cds not found: query %s.\n" % p.mQueryToken )
continue
map_query2sbjct, genomic_fragment = Genomics.Alignment2CDNA( p.mMapPeptide2Genome,
query_from = p.mQueryFrom,
sbjct_from = 0,
genome = genomic_fragment )
## check for errors:
if map_query2sbjct.getRowTo() != p.mQueryTo * 3:
options.stdlog.write( "# ERROR: boundary shift in query at line %s\n# %i %i\n" % (line, map_query2sbjct.getRowTo(), p.mQueryTo * 3 ) )
if map_query2sbjct.getColTo() > len(genomic_fragment):
options.stdlog.write( "# ERROR: length mismatch in line %s\n# genomic fragment (%i) shorter than last aligned residue (%i)\n" %\
(line, len(genomic_fragment), map_query2sbjct.getColTo()) )
options.stdlog.write( "# cds %s\n# genomic %s\n" % (str( cds_fragment ), genomic_fragment ))
nlength += 1
continue
if map_query2sbjct.getRowTo() > len(cds_fragment):
options.stdlog.write( "# ERROR: length mismatch in line %s\n# cds fragment (%i) shorter than last aligned residue (%i)\n" %\
(line, len(cds_fragment), map_query2sbjct.getRowTo()) )
options.stdlog.write( "# cds %s\n# genomic %s\n" % (str( cds_fragment ), genomic_fragment ))
nlength += 1
continue
cds_seq = alignlib_lite.makeSequence( cds_fragment )
genomic_seq = alignlib_lite.makeSequence( genomic_fragment )
f = alignlib_lite.AlignmentFormatExplicit( map_query2sbjct, cds_seq, genomic_seq )
row_ali = f.mRowAlignment
col_ali = f.mColAlignment
row_ali, col_ali = Genomics.RemoveFrameShiftsFromAlignment(row_ali, col_ali)
row_ali = Genomics.MaskStopCodons( row_ali )
col_ali = Genomics.MaskStopCodons( col_ali )
if len(row_ali) != len(col_ali):
options.stdlog.write( "# ERROR: wrong alignment lengths.\n" )
sys.exit(1)
if len(row_ali) % 3 or len(col_ali) % 3:
options.stdlog.write( "# ERROR: sequences are not a multiple of 3 in line: %s\n" % line )
options.stdlog.write( "# %6i %s\n# %6i %s\n" % (len(row_ali), str(row_ali), len(col_ali), str(col_ali) ) )
n3 += 1
input = re.sub( "[-X]", "", p.mTranslation )
ref = re.sub( "[-X]", "", Genomics.TranslateDNA2Protein( col_ali ) )
if input != ref:
if options.loglevel >= 1:
options.stdlog.write("# sanity check failed for %s - %s\n# %6i %s\n# %6i %s\n" % (p.mPredictionId, p.mQueryToken,
len(input), input,
len(ref), ref ) )
nsanity += 1
continue
options.stdout.write( ">%s\n%s\n" % (p.mPredictionId, row_ali) )
options.stdout.write( ">%s_vs_%s_%s_%i_%i\n%s\n" % \
(p.mQueryToken, p.mSbjctToken, p.mSbjctStrand, p.mSbjctGenomeFrom, p.mSbjctGenomeTo, col_ali) )
noutput += 1
if options.loglevel >= 1:
options.stdlog.write("# ninput=%i, noutput=%i, nsanity=%i, nlength=%i, n3=%i\n" % (ninput, noutput, nsanity, nlength, n3) )
E.Stop()
