map_row2col.clear()
alignlib_lite.AlignmentFormatExplicit(
link.mQueryFrom, link.mQueryAli, link.mSbjctFrom,
link.mSbjctAli).copy(map_row2col)
# test all combinations, the alignment might be a suboptimal alignment in case
# of repeats.
for e1 in cds[link.mQueryToken]:
for e2 in cds[link.mSbjctToken]:
tmp_map_row2col.clear()
if param_expand:
alignlib_lite.copyAlignment(
tmp_map_row2col,
map_row2col,
e1.mPeptideFrom + 1,
e1.mPeptideTo,
e2.mPeptideFrom + 1,
e2.mPeptideTo,
)
else:
alignlib_lite.copyAlignment(tmp_map_row2col,
map_row2col,
e1.mPeptideFrom / 3 + 1,
e1.mPeptideTo / 3 + 1,
e2.mPeptideFrom / 3 + 1,
e2.mPeptideTo / 3 + 1)
# in case of split codons, there is an alignment of length
# 1. Skip that.
if tmp_map_row2col.getLength() > 1:
link.mQueryAli = ScaleAlignment( link.mQueryAli, 3 )
link.mSbjctAli = ScaleAlignment( link.mSbjctAli, 3 )
map_row2col.clear()
alignlib_lite.AlignmentFormatExplicit(
link.mQueryFrom, link.mQueryAli,
link.mSbjctFrom, link.mSbjctAli ).copy( map_row2col )
## test all combinations, the alignment might be a suboptimal alignment in case
## of repeats.
for e1 in cds[link.mQueryToken]:
for e2 in cds[link.mSbjctToken]:
tmp_map_row2col.clear()
if param_expand:
alignlib_lite.copyAlignment( tmp_map_row2col, map_row2col,
e1.mPeptideFrom + 1, e1.mPeptideTo,
e2.mPeptideFrom + 1, e2.mPeptideTo,
)
else:
alignlib_lite.copyAlignment( tmp_map_row2col, map_row2col,
e1.mPeptideFrom / 3 + 1, e1.mPeptideTo / 3 + 1,
e2.mPeptideFrom / 3 + 1, e2.mPeptideTo / 3 + 1)
## in case of split codons, there is an alignment of length 1. Skip that.
if tmp_map_row2col.getLength() > 1:
print string.join( map(str, (link.mQueryToken, e1.mRank,
link.mSbjctToken, e2.mRank,
link.mEvalue,
alignlib_lite.AlignmentFormatEmissions( tmp_map_row2col ))), "\t" )
npairs += 1
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/compare_predictions2exons.py 2011 2008-07-04 10:40:51Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome.")
parser.add_option("-b",
"--boundaries",
dest="filename_boundaries",
type="string",
help="filename with exon boundaries.")
parser.add_option("-e",
"--exons",
dest="filename_exons",
type="string",
help="filename with exons (output).")
parser.add_option("-p",
"--peptides",
dest="filename_peptides",
type="string",
help="filename with peptide sequences.")
parser.add_option(
"-w",
"--write-notfound",
dest="write_notfound",
action="store_true",
help="print exons for predictions not found in reference.")
parser.add_option("-q",
"--quality-pide",
dest="quality_threshold_pide",
type="int",
help="quality threshold (pide) for exons.")
parser.set_defaults(
genome_file="genome",
filename_boundaries=None,
filename_exons=None,
filename_peptides=None,
quality_threshold_pide=0,
write_notfound=False,
## allowed number of nucleotides for exon boundaries to
## be considered equivalent.
slipping_exon_boundary=9,
## stop codons to search for
stop_codons=("TAG", "TAA", "TGA"),
)
(options, args) = E.Start(parser, add_pipe_options=True)
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
reference_exon_boundaries = {}
if options.filename_boundaries:
reference_exon_boundaries = Exons.ReadExonBoundaries(open(
options.filename_boundaries, "r"),
do_invert=1,
remove_utr=1)
E.info("read exon boundaries for %i queries" %
len(reference_exon_boundaries))
if options.filename_exons:
outfile_exons = open(options.filename_exons, "w")
outfile_exons.write("%s\n" % "\t".join(
("prediction_id", "exon_id", "exon_from", "exon_to", "exon_frame",
"reference_id", "reference_from", "reference_to",
"reference_phase", "pidentity", "psimilarity", "nframeshifts",
"ngaps", "nstopcodons", "is_ok", "genome_exon_from",
"genome_exon_to")))
else:
outfile_exons = None
if options.filename_peptides:
peptide_sequences = Genomics.ReadPeptideSequences(
open(options.filename_peptides, "r"))
E.info("read peptide sequences for %i queries" %
len(peptide_sequences))
else:
peptide_sequences = {}
entry = PredictionParser.PredictionParserEntry()
last_filename_genome = None
nfound, nmissed_exons, nmissed_length = 0, 0, 0
nempty_alignments = 0
fasta = IndexedFasta.IndexedFasta(options.genome_file)
options.stdout.write("%s\n" % "\t".join(
("prediction_id", "number", "dubious_exons", "boundaries_sum",
"boundaries_max", "identical_exons", "inserted_exons",
"deleted_exons", "inserted_introns", "deleted_introns",
"truncated_Nterminus", "truncated_Cterminus", "deleted_Nexons",
"deleted_Cexons", "inserted_Nexons", "inserted_Cexons")))
for line in sys.stdin:
if line[0] == "#": continue
try:
entry.Read(line)
except ValueError, msg:
print "# parsing failed with msg %s in line %s" % (msg, line[:-1])
sys.exit(1)
exons = Genomics.Alignment2ExonBoundaries(
entry.mMapPeptide2Genome,
query_from=entry.mQueryFrom,
sbjct_from=entry.mSbjctGenomeFrom,
add_stop_codon=0)
if exons[-1][4] != entry.mSbjctGenomeTo:
print "# WARNING: discrepancy in exon calculation!!!"
for e in exons:
print "#", str(e)
print "#", str(entry)
if options.loglevel >= 5:
for e in exons:
print "#", str(e)
genomic_fragment = fasta.getSequence(entry.mSbjctToken,
entry.mSbjctStrand,
entry.mSbjctGenomeFrom,
entry.mSbjctGenomeTo)
skip = False
if peptide_sequences.has_key(entry.mQueryToken):
query_sequence = alignlib_lite.makeSequence(
peptide_sequences[entry.mQueryToken])
sbjct_sequence = alignlib_lite.makeSequence(entry.mTranslation)
percent_similarity, percent_identity = 0, 0
if query_sequence.getLength(
) < entry.mMapPeptide2Translation.getRowTo():
print "# WARNING: query sequence %s is too short: %i %i" % (
entry.mQueryToken, query_sequence.getLength(),
entry.mMapPeptide2Translation.getRowTo())
sys.stdout.flush()
nmissed_length += 1
skip = True
elif sbjct_sequence.getLength(
) < entry.mMapPeptide2Translation.getColTo():
print "# WARNING: sbjct sequence %s is too short: %i %i" % (
entry.mSbjctToken, sbjct_sequence.getLength(),
entry.mMapPeptide2Translation.getColTo())
sys.stdout.flush()
nmissed_length += 1
skip = True
else:
alignlib_lite.rescoreAlignment(
entry.mMapPeptide2Translation, query_sequence,
sbjct_sequence,
alignlib_lite.makeScorer(query_sequence, sbjct_sequence))
percent_identity = alignlib_lite.calculatePercentIdentity(
entry.mMapPeptide2Translation, query_sequence,
sbjct_sequence) * 100
percent_similarity = alignlib_lite.calculatePercentSimilarity(
entry.mMapPeptide2Translation) * 100
E.debug(
"prediction %s: percent identity/similarity: before=%5.2f/%5.2f, realigned=%5.2f/%5.2f"
%
(str(entry.mPredictionId), entry.mPercentSimilarity,
entry.mPercentIdentity, percent_similarity, percent_identity))
else:
query_sequence = None
sbjct_sequence = None
# default values
exons_num_exons = "na"
exons_boundaries_sum = "na"
exons_boundaries_max = "na"
dubious_exons = "na"
ndeleted_exons, ninserted_exons, ndeleted_introns, ninserted_introns, nidentical_exons = 0, 0, 0, 0, 0
truncated_Nterminal_exon, truncated_Cterminal_exon = 0, 0
ndeleted_Nexons, ndeleted_Cexons = 0, 0
ninserted_Nexons, ninserted_Cexons = 0, 0
exons_offset = exons[0][3]
if not reference_exon_boundaries.has_key(entry.mQueryToken):
print "# WARNING: sequence %s has no exon boundaries" % (
entry.mQueryToken)
sys.stdout.flush()
nmissed_exons += 1
skip = True
if not skip:
nfound += 1
ref_exons = reference_exon_boundaries[entry.mQueryToken]
ref_exons_offset = ref_exons[0].mGenomeFrom
exons_num_exons = len(ref_exons) - len(exons)
exons_boundaries_sum = 0
exons_phase = 0
exons_boundaries_max = 0
dubious_exons = 0
inserted_exons = 0
temp_inserted_exons = 0
if options.loglevel >= 3:
for e in exons:
options.stdlog.write("# %s\n" % str(e))
for e in ref_exons:
options.stdlog.write("# %s\n" % str(e))
min_pide = entry.mPercentIdentity * options.quality_threshold_pide / 100
in_sync = 0
e, r = 0, 0
while e < len(exons) and r < len(ref_exons):
this_e, this_r = e + 1, r + 1
percent_identity = 0
percent_similarity = 0
is_good_exon = 0
if options.loglevel >= 4:
options.stdlog.write("# current exons: %i and %i\n" %
(e, r))
sys.stdout.flush()
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to, exon_ali = exons[
e][0:6]
ref_from, ref_to, ref_phase, ref_genome_from, ref_genome_to = (
ref_exons[r].mPeptideFrom, ref_exons[r].mPeptideTo,
ref_exons[r].frame, ref_exons[r].mGenomeFrom,
ref_exons[r].mGenomeTo)
ref_genome_from -= ref_exons_offset
ref_genome_to -= ref_exons_offset
## get percent identity for exon
exon_percent_identity = 0
exon_percent_similarity = 0
if query_sequence and sbjct_sequence:
tmp_ali = alignlib_lite.makeAlignmentVector()
xquery_from = exon_from / 3
xquery_to = exon_to / 3
alignlib_lite.copyAlignment(tmp_ali,
entry.mMapPeptide2Translation,
xquery_from, xquery_to)
if tmp_ali.getLength() == 0:
options.stdlog.write(
"# WARNING: empty alignment %s\n" % str(
(ref_from, exon_from, ref_to, exon_to,
xquery_from, xquery_to)))
nempty_alignments += 1
else:
if options.loglevel >= 5:
options.stdlog.write("# %s\n" % str(
alignlib_lite.AlignmentFormatExplicit(
tmp_ali, query_sequence, sbjct_sequence)))
exon_percent_identity = alignlib_lite.calculatePercentIdentity(
tmp_ali, query_sequence, sbjct_sequence) * 100
exon_percent_similarity = alignlib_lite.calculatePercentSimilarity(
tmp_ali) * 100
if exon_percent_identity >= min_pide:
is_good_exon = 1
else:
is_good_exon = 0
if e < len(exons) - 1:
(next_exon_from, next_exon_to, next_exon_phase,
next_exon_genome_from, next_exon_genome_to,
next_exon_ali) = exons[e + 1][0:6]
else:
(next_exon_from, next_exon_to, next_exon_phase,
next_exon_genome_from, next_exon_genome_to,
next_exon_ali) = 0, 0, 0, 0, 0, []
if r < len(ref_exons) - 1:
next_ref_from, next_ref_to, next_ref_phase = (
ref_exons[r + 1].mPeptideFrom,
ref_exons[r + 1].mPeptideTo, ref_exons[r + 1].frame)
else:
next_ref_from, next_ref_to, next_ref_phase = 0, 0, 0
if options.loglevel >= 2:
options.stdlog.write("# %s\n" % "\t".join(
map(str, (entry.mQueryToken, exon_from, exon_to,
exon_phase, exon_genome_from, exon_genome_to,
ref_from, ref_to, ref_phase))))
sys.stdout.flush()
# beware of small exons.
# if less than options.slipping_exon_boundary: boundary is 0
# check if end is more than options.splipping_exon_boundary apart as well.
if exon_to - exon_from <= options.slipping_exon_boundary or \
ref_to - ref_from <= options.slipping_exon_boundary:
boundary = 0
else:
boundary = options.slipping_exon_boundary
if ref_to <= exon_from + boundary and \
ref_to <= exon_to - options.slipping_exon_boundary:
## no overlap
is_good_exon = 0
if e == 0:
ndeleted_Nexons += 1
else:
ndeleted_exons += 1
r += 1
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to = 0, 0, 0, 0, 0
overlap = 0
elif exon_to <= ref_from + boundary and \
exon_to <= ref_to - options.slipping_exon_boundary:
## no overlap
is_good_exon = 0
if r == 0:
ninserted_Nexons += 1
else:
ninserted_exons += 1
e += 1
ref_from, ref_to, ref_phase = 0, 0, 0
overlap = 0
else:
## overlap
overlap = 1
dfrom = int(math.fabs(exon_from - ref_from))
dto = int(math.fabs(exon_to - ref_to))
## get percent identity for overlapping fragment
if query_sequence and sbjct_sequence:
## this the problem
tmp_ali = alignlib_lite.makeAlignmentVector()
xquery_from = max(ref_from / 3, exon_from / 3)
xquery_to = min(ref_to / 3, exon_to / 3)
alignlib_lite.copyAlignment(
tmp_ali, entry.mMapPeptide2Translation,
xquery_from, xquery_to)
if tmp_ali.getLength() == 0:
options.stdlog.write(
"# warning: empty alignment %s\n" % str(
(ref_from, exon_from, ref_to, exon_to,
xquery_from, xquery_to)))
percent_identity = 0
percent_similarity = 0
else:
if options.loglevel >= 5:
print str(
alignlib_lite.AlignmentFormatExplicit(
tmp_ali, query_sequence,
sbjct_sequence))
percent_identity = alignlib_lite.calculatePercentIdentity(
tmp_ali, query_sequence, sbjct_sequence) * 100
percent_similarity = alignlib_lite.calculatePercentSimilarity(
tmp_ali) * 100
if percent_identity >= min_pide:
is_good_exon = 1
else:
is_good_exon = 0
dubious_exons += 1
## adjust regions for terminal exons
if e == 0 and r == 0 and dfrom <= (entry.mQueryFrom -
1) * 3 and dfrom > 0:
if is_good_exon:
truncated_Nterminal_exon = dfrom
dfrom = 0
## truncated terminal exons
if e == len(exons) - 1 and r == len(
ref_exons) - 1 and dto <= (
entry.mQueryLength -
entry.mQueryTo) * 3 and dto > 0:
if is_good_exon:
truncated_Cterminal_exon = dto
dto = 0
## do not count deviations for terminal query exons
if e == 0 and dfrom <= entry.mQueryFrom * 3 and dfrom > 0:
dfrom = 0
if e == len(exons) - 1 and dto <= (
entry.mQueryLength -
entry.mQueryTo) * 3 and dto > 0:
dto = 0
## permit difference of one codon (assumed to be stop)
if e == len(exons) - 1 and r == len(
ref_exons) - 1 and dto == 3:
dto = 0
## deal with different boundary conditions:
if dfrom == 0 and dto == 0:
if is_good_exon: nidentical_exons += 1
e += 1
r += 1
## next exon within this ref_exon
elif exon_to < ref_to and next_exon_to and next_exon_to <= ref_to + options.slipping_exon_boundary:
if is_good_exon: ninserted_introns += 1
e += 1
in_sync = 1
dto = 0
## next ref_exon within this exon
elif ref_to < exon_to and next_ref_to and next_ref_to <= exon_to + options.slipping_exon_boundary:
if is_good_exon: ndeleted_introns += 1
r += 1
in_sync = 1
dto = 0
else:
e += 1
r += 1
if in_sync:
dfrom = 0
if is_good_exon:
exons_boundaries_sum += dfrom + dto
exons_boundaries_max = max(dfrom, exons_boundaries_max)
exons_boundaries_max = max(dto, exons_boundaries_max)
###########################################################
## count inserted/deleted introns and misplaced boundaries
##
## if exon and next_exon in ref_exon: inserted intron
## if ref_exon and next_ref_exon in exon: deleted intron
if outfile_exons:
if genomic_fragment and exon_genome_to:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons, disruptions = Genomics.CountGeneFeatures(
exon_genome_from - entry.mSbjctGenomeFrom,
exon_ali,
genomic_fragment,
border_stop_codon=0)
else:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons = 0, 0, 0, 0, 0
if exon_to == 0: this_e = 0
if ref_to == 0: this_r = 0
outfile_exons.write(
string.join(
map(str, (
entry.mPredictionId,
this_e,
exon_from,
exon_to,
exon_phase,
this_r,
ref_from,
ref_to,
ref_phase,
percent_identity,
percent_similarity,
nframeshifts,
ngaps,
nstopcodons,
is_good_exon,
exon_genome_from,
exon_genome_to,
)), "\t") + "\n")
while e < len(exons):
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to = exons[
e][0:5]
e += 1
ninserted_Cexons += 1
if outfile_exons:
outfile_exons.write(
string.join(
map(str, (
entry.mPredictionId,
e,
exon_from,
exon_to,
exon_phase,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
exon_genome_from,
exon_genome_to,
)), "\t") + "\n")
while r < len(ref_exons):
ref_from, ref_to, ref_phase, ref_genome_from, ref_genome_to = (
ref_exons[r].mPeptideFrom, ref_exons[r].mPeptideTo,
ref_exons[r].frame, ref_exons[r].mGenomeFrom,
ref_exons[r].mGenomeTo)
ndeleted_Cexons += 1
ref_genome_from -= ref_exons_offset
ref_genome_to -= ref_exons_offset
r += 1
if outfile_exons:
outfile_exons.write(
string.join(
map(str, (
entry.mPredictionId,
0,
0,
0,
0,
r,
ref_from,
ref_to,
ref_phase,
0,
0,
0,
0,
0,
0,
0,
0,
)), "\t") + "\n")
else:
if options.write_notfound:
this_e = 0
## use prediction's identity/similarity for exons.
## This will still then flag stop-codons in later analysis
percent_identity = entry.mPercentIdentity
percent_similarity = entry.mPercentSimilarity
for exon in exons:
this_e += 1
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to, exon_ali = exon[
0:6]
if genomic_fragment:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons, disruptions = Genomics.CountGeneFeatures(
exon_genome_from - entry.mSbjctGenomeFrom,
exon_ali, genomic_fragment)
outfile_exons.write(
string.join(
map(str, (
entry.mPredictionId,
this_e,
exon_from,
exon_to,
exon_phase,
0,
0,
0,
0,
percent_identity,
percent_similarity,
nframeshifts,
ngaps,
nstopcodons,
1,
exon_genome_from,
exon_genome_to,
)), "\t") + "\n")
options.stdout.write("\t".join(
map(str, (entry.mPredictionId, exons_num_exons, dubious_exons,
exons_boundaries_sum, exons_boundaries_max,
nidentical_exons, ninserted_exons, ndeleted_exons,
ninserted_introns, ndeleted_introns,
truncated_Nterminal_exon, truncated_Cterminal_exon,
ndeleted_Nexons, ndeleted_Cexons, ninserted_Nexons,
ninserted_Cexons))) + "\n")
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/compare_predictions2exons.py 2011 2008-07-04 10:40:51Z andreas $",
usage = globals()["__doc__"] )
parser.add_option( "-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome." )
parser.add_option( "-b", "--boundaries", dest="filename_boundaries", type="string",
help="filename with exon boundaries." )
parser.add_option( "-e", "--exons", dest="filename_exons", type="string",
help="filename with exons (output)." )
parser.add_option( "-p", "--peptides", dest="filename_peptides", type="string",
help="filename with peptide sequences." )
parser.add_option( "-w", "--write-notfound", dest="write_notfound", action="store_true",
help="print exons for predictions not found in reference." )
parser.add_option( "-q", "--quality-pide", dest="quality_threshold_pide", type="int",
help="quality threshold (pide) for exons." )
parser.set_defaults(
genome_file = "genome",
filename_boundaries = None,
filename_exons = None,
filename_peptides = None,
quality_threshold_pide = 0,
write_notfound = False,
## allowed number of nucleotides for exon boundaries to
## be considered equivalent.
slipping_exon_boundary = 9,
## stop codons to search for
stop_codons = ("TAG", "TAA", "TGA"), )
(options, args) = E.Start( parser, add_pipe_options = True )
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
reference_exon_boundaries = {}
if options.filename_boundaries:
reference_exon_boundaries = Exons.ReadExonBoundaries( open( options.filename_boundaries, "r"),
do_invert = 1,
remove_utr = 1)
E.info( "read exon boundaries for %i queries" % len(reference_exon_boundaries) )
if options.filename_exons:
outfile_exons = open( options.filename_exons, "w")
outfile_exons.write( "%s\n" % "\t".join( (
"prediction_id",
"exon_id",
"exon_from",
"exon_to",
"exon_frame",
"reference_id",
"reference_from",
"reference_to",
"reference_phase",
"pidentity",
"psimilarity",
"nframeshifts",
"ngaps",
"nstopcodons",
"is_ok",
"genome_exon_from",
"genome_exon_to") ) )
else:
outfile_exons = None
if options.filename_peptides:
peptide_sequences = Genomics.ReadPeptideSequences( open(options.filename_peptides, "r") )
E.info("read peptide sequences for %i queries" % len(peptide_sequences) )
else:
peptide_sequences = {}
entry = PredictionParser.PredictionParserEntry()
last_filename_genome = None
nfound, nmissed_exons, nmissed_length = 0, 0, 0
nempty_alignments = 0
fasta = IndexedFasta.IndexedFasta( options.genome_file )
options.stdout.write( "%s\n" % "\t".join( (
"prediction_id",
"number",
"dubious_exons",
"boundaries_sum",
"boundaries_max",
"identical_exons",
"inserted_exons",
"deleted_exons",
"inserted_introns",
"deleted_introns",
"truncated_Nterminus",
"truncated_Cterminus",
"deleted_Nexons",
"deleted_Cexons",
"inserted_Nexons",
"inserted_Cexons" ) ) )
for line in sys.stdin:
if line[0] == "#": continue
try:
entry.Read(line)
except ValueError, msg:
print "# parsing failed with msg %s in line %s" % (msg, line[:-1])
sys.exit(1)
exons = Genomics.Alignment2ExonBoundaries( entry.mMapPeptide2Genome,
query_from = entry.mQueryFrom,
sbjct_from = entry.mSbjctGenomeFrom,
add_stop_codon = 0 )
if exons[-1][4] != entry.mSbjctGenomeTo:
print "# WARNING: discrepancy in exon calculation!!!"
for e in exons:
print "#", str(e)
print "#", str(entry)
if options.loglevel >= 5:
for e in exons:
print "#", str(e)
genomic_fragment = fasta.getSequence( entry.mSbjctToken, entry.mSbjctStrand,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo )
skip = False
if peptide_sequences.has_key( entry.mQueryToken ):
query_sequence = alignlib_lite.makeSequence(peptide_sequences[entry.mQueryToken])
sbjct_sequence = alignlib_lite.makeSequence(entry.mTranslation)
percent_similarity, percent_identity = 0, 0
if query_sequence.getLength() < entry.mMapPeptide2Translation.getRowTo():
print "# WARNING: query sequence %s is too short: %i %i" % ( entry.mQueryToken,
query_sequence.getLength(),
entry.mMapPeptide2Translation.getRowTo())
sys.stdout.flush()
nmissed_length += 1
skip = True
elif sbjct_sequence.getLength() < entry.mMapPeptide2Translation.getColTo():
print "# WARNING: sbjct sequence %s is too short: %i %i" % ( entry.mSbjctToken,
sbjct_sequence.getLength(),
entry.mMapPeptide2Translation.getColTo())
sys.stdout.flush()
nmissed_length += 1
skip = True
else:
alignlib_lite.rescoreAlignment( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence,
alignlib_lite.makeScorer( query_sequence, sbjct_sequence ) )
percent_identity = alignlib_lite.calculatePercentIdentity( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence ) * 100
percent_similarity = alignlib_lite.calculatePercentSimilarity( entry.mMapPeptide2Translation ) * 100
E.debug( "prediction %s: percent identity/similarity: before=%5.2f/%5.2f, realigned=%5.2f/%5.2f" % (
str(entry.mPredictionId),
entry.mPercentSimilarity,
entry.mPercentIdentity,
percent_similarity,
percent_identity ) )
else:
query_sequence = None
sbjct_sequence = None
# default values
exons_num_exons = "na"
exons_boundaries_sum = "na"
exons_boundaries_max = "na"
dubious_exons = "na"
ndeleted_exons, ninserted_exons, ndeleted_introns, ninserted_introns, nidentical_exons = 0,0,0,0,0
truncated_Nterminal_exon, truncated_Cterminal_exon = 0,0
ndeleted_Nexons, ndeleted_Cexons = 0, 0
ninserted_Nexons, ninserted_Cexons = 0, 0
exons_offset = exons[0][3]
if not reference_exon_boundaries.has_key( entry.mQueryToken ):
print "# WARNING: sequence %s has no exon boundaries" % ( entry.mQueryToken )
sys.stdout.flush()
nmissed_exons += 1
skip = True
if not skip:
nfound += 1
ref_exons = reference_exon_boundaries[entry.mQueryToken]
ref_exons_offset = ref_exons[0].mGenomeFrom
exons_num_exons = len(ref_exons) - len(exons)
exons_boundaries_sum = 0
exons_phase = 0
exons_boundaries_max = 0
dubious_exons = 0
inserted_exons = 0
temp_inserted_exons = 0
if options.loglevel >= 3:
for e in exons:
options.stdlog.write( "# %s\n" % str(e) )
for e in ref_exons:
options.stdlog.write( "# %s\n" % str(e) )
min_pide = entry.mPercentIdentity * options.quality_threshold_pide / 100
in_sync = 0
e,r = 0,0
while e < len(exons) and r < len(ref_exons):
this_e, this_r = e+1, r+1
percent_identity = 0
percent_similarity = 0
is_good_exon = 0
if options.loglevel >= 4:
options.stdlog.write( "# current exons: %i and %i\n" % (e, r) )
sys.stdout.flush()
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to, exon_ali = exons[e][0:6]
ref_from, ref_to, ref_phase, ref_genome_from, ref_genome_to = (ref_exons[r].mPeptideFrom,
ref_exons[r].mPeptideTo,
ref_exons[r].frame,
ref_exons[r].mGenomeFrom,
ref_exons[r].mGenomeTo)
ref_genome_from -= ref_exons_offset
ref_genome_to -= ref_exons_offset
## get percent identity for exon
exon_percent_identity = 0
exon_percent_similarity = 0
if query_sequence and sbjct_sequence:
tmp_ali = alignlib_lite.makeAlignmentVector()
xquery_from = exon_from / 3
xquery_to = exon_to / 3
alignlib_lite.copyAlignment( tmp_ali, entry.mMapPeptide2Translation, xquery_from, xquery_to )
if tmp_ali.getLength() == 0:
options.stdlog.write( "# WARNING: empty alignment %s\n" % str((ref_from, exon_from, ref_to, exon_to, xquery_from, xquery_to)))
nempty_alignments += 1
else:
if options.loglevel >= 5:
options.stdlog.write( "# %s\n" % str( alignlib_lite.AlignmentFormatExplicit( tmp_ali, query_sequence, sbjct_sequence ) ) )
exon_percent_identity = alignlib_lite.calculatePercentIdentity( tmp_ali,
query_sequence,
sbjct_sequence ) * 100
exon_percent_similarity = alignlib_lite.calculatePercentSimilarity( tmp_ali ) * 100
if exon_percent_identity >= min_pide:
is_good_exon = 1
else:
is_good_exon = 0
if e < len(exons) -1 :
(next_exon_from, next_exon_to, next_exon_phase,
next_exon_genome_from, next_exon_genome_to, next_exon_ali) = exons[e+1][0:6]
else:
(next_exon_from, next_exon_to, next_exon_phase,
next_exon_genome_from, next_exon_genome_to, next_exon_ali) = 0, 0, 0, 0, 0, []
if r < len(ref_exons) - 1:
next_ref_from, next_ref_to, next_ref_phase = (ref_exons[r+1].mPeptideFrom,
ref_exons[r+1].mPeptideTo,
ref_exons[r+1].frame)
else:
next_ref_from, next_ref_to, next_ref_phase = 0, 0, 0
if options.loglevel >= 2:
options.stdlog.write( "# %s\n" % "\t".join( map(str, (entry.mQueryToken,
exon_from, exon_to, exon_phase,
exon_genome_from, exon_genome_to,
ref_from, ref_to, ref_phase ))))
sys.stdout.flush()
# beware of small exons.
# if less than options.slipping_exon_boundary: boundary is 0
# check if end is more than options.splipping_exon_boundary apart as well.
if exon_to - exon_from <= options.slipping_exon_boundary or \
ref_to - ref_from <= options.slipping_exon_boundary:
boundary = 0
else:
boundary = options.slipping_exon_boundary
if ref_to <= exon_from + boundary and \
ref_to <= exon_to - options.slipping_exon_boundary:
## no overlap
is_good_exon = 0
if e == 0:
ndeleted_Nexons += 1
else:
ndeleted_exons += 1
r += 1
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to = 0, 0, 0, 0, 0
overlap = 0
elif exon_to <= ref_from + boundary and \
exon_to <= ref_to - options.slipping_exon_boundary:
## no overlap
is_good_exon = 0
if r == 0:
ninserted_Nexons += 1
else:
ninserted_exons += 1
e += 1
ref_from, ref_to, ref_phase = 0, 0, 0
overlap = 0
else:
## overlap
overlap = 1
dfrom = int(math.fabs(exon_from - ref_from))
dto = int(math.fabs(exon_to - ref_to))
## get percent identity for overlapping fragment
if query_sequence and sbjct_sequence:
## this the problem
tmp_ali = alignlib_lite.makeAlignmentVector()
xquery_from = max( ref_from / 3, exon_from / 3)
xquery_to = min(ref_to / 3, exon_to / 3)
alignlib_lite.copyAlignment( tmp_ali, entry.mMapPeptide2Translation, xquery_from, xquery_to )
if tmp_ali.getLength() == 0:
options.stdlog.write( "# warning: empty alignment %s\n" % str((ref_from, exon_from, ref_to, exon_to, xquery_from, xquery_to )))
percent_identity = 0
percent_similarity = 0
else:
if options.loglevel >= 5:
print str( alignlib_lite.AlignmentFormatExplicit( tmp_ali, query_sequence, sbjct_sequence ) )
percent_identity = alignlib_lite.calculatePercentIdentity( tmp_ali,
query_sequence,
sbjct_sequence ) * 100
percent_similarity = alignlib_lite.calculatePercentSimilarity( tmp_ali ) * 100
if percent_identity >= min_pide:
is_good_exon = 1
else:
is_good_exon = 0
dubious_exons += 1
## adjust regions for terminal exons
if e == 0 and r == 0 and dfrom <= (entry.mQueryFrom - 1) * 3 and dfrom > 0:
if is_good_exon:
truncated_Nterminal_exon = dfrom
dfrom = 0
## truncated terminal exons
if e == len(exons)-1 and r == len(ref_exons)-1 and dto <= (entry.mQueryLength - entry.mQueryTo) * 3 and dto > 0:
if is_good_exon:
truncated_Cterminal_exon = dto
dto = 0
## do not count deviations for terminal query exons
if e == 0 and dfrom <= entry.mQueryFrom * 3 and dfrom > 0:
dfrom = 0
if e == len(exons)-1 and dto <= (entry.mQueryLength - entry.mQueryTo) * 3 and dto > 0:
dto = 0
## permit difference of one codon (assumed to be stop)
if e == len(exons)-1 and r == len(ref_exons)-1 and dto == 3:
dto = 0
## deal with different boundary conditions:
if dfrom == 0 and dto == 0:
if is_good_exon: nidentical_exons += 1
e += 1
r += 1
## next exon within this ref_exon
elif exon_to < ref_to and next_exon_to and next_exon_to <= ref_to + options.slipping_exon_boundary:
if is_good_exon: ninserted_introns += 1
e += 1
in_sync = 1
dto = 0
## next ref_exon within this exon
elif ref_to < exon_to and next_ref_to and next_ref_to <= exon_to + options.slipping_exon_boundary:
if is_good_exon: ndeleted_introns += 1
r += 1
in_sync = 1
dto = 0
else:
e += 1
r += 1
if in_sync:
dfrom = 0
if is_good_exon:
exons_boundaries_sum += dfrom + dto
exons_boundaries_max = max( dfrom, exons_boundaries_max )
exons_boundaries_max = max( dto, exons_boundaries_max )
###########################################################
## count inserted/deleted introns and misplaced boundaries
##
## if exon and next_exon in ref_exon: inserted intron
## if ref_exon and next_ref_exon in exon: deleted intron
if outfile_exons:
if genomic_fragment and exon_genome_to:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons, disruptions = Genomics.CountGeneFeatures( exon_genome_from - entry.mSbjctGenomeFrom,
exon_ali,
genomic_fragment,
border_stop_codon = 0
)
else:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons = 0, 0, 0, 0, 0
if exon_to == 0: this_e = 0
if ref_to == 0: this_r = 0
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
this_e, exon_from, exon_to, exon_phase,
this_r, ref_from, ref_to, ref_phase,
percent_identity, percent_similarity,
nframeshifts, ngaps, nstopcodons,
is_good_exon,
exon_genome_from, exon_genome_to,
)), "\t") + "\n")
while e < len(exons):
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to = exons[e][0:5]
e += 1
ninserted_Cexons += 1
if outfile_exons:
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
e, exon_from, exon_to, exon_phase,
0, 0, 0, 0,
0, 0,
0, 0, 0,
1,
exon_genome_from, exon_genome_to,
)), "\t") + "\n")
while r < len(ref_exons):
ref_from, ref_to, ref_phase, ref_genome_from, ref_genome_to = (ref_exons[r].mPeptideFrom,
ref_exons[r].mPeptideTo,
ref_exons[r].frame,
ref_exons[r].mGenomeFrom,
ref_exons[r].mGenomeTo)
ndeleted_Cexons += 1
ref_genome_from -= ref_exons_offset
ref_genome_to -= ref_exons_offset
r += 1
if outfile_exons:
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
0, 0, 0, 0,
r, ref_from, ref_to, ref_phase,
0, 0,
0, 0, 0,
0,
0, 0,
)), "\t") + "\n")
else:
if options.write_notfound:
this_e = 0
## use prediction's identity/similarity for exons.
## This will still then flag stop-codons in later analysis
percent_identity = entry.mPercentIdentity
percent_similarity = entry.mPercentSimilarity
for exon in exons:
this_e += 1
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to, exon_ali = exon[0:6]
if genomic_fragment:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons, disruptions = Genomics.CountGeneFeatures( exon_genome_from - entry.mSbjctGenomeFrom,
exon_ali,
genomic_fragment )
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
this_e, exon_from, exon_to, exon_phase,
0, 0, 0, 0,
percent_identity, percent_similarity,
nframeshifts, ngaps, nstopcodons,
1,
exon_genome_from, exon_genome_to,
)), "\t") + "\n")
options.stdout.write( "\t".join(map(str,
(entry.mPredictionId,
exons_num_exons,
dubious_exons,
exons_boundaries_sum,
exons_boundaries_max,
nidentical_exons,
ninserted_exons, ndeleted_exons,
ninserted_introns, ndeleted_introns,
truncated_Nterminal_exon, truncated_Cterminal_exon,
ndeleted_Nexons, ndeleted_Cexons,
ninserted_Nexons, ninserted_Cexons))) + "\n" )
