def CheckResult( self,
result,
info1, info2):
"""check if result is ok. Check for each fragment, if it overlaps
with the domains to be tested and dump if ok. This simulates
psiblast.
"""
row_from, row_to = map(string.atoi, info1[1:3])
col_from, col_to = map(string.atoi, info2[1:3])
## check for overlap
for fragment in self.mFragments:
# print alignlib.writeAlignataTable( fragment, 8, 1)
xcol_from = Tools.MapRight(fragment, row_from )
xcol_to = Tools.MapLeft(fragment, row_to )
overlap = min(col_to, xcol_to) - max(col_from, xcol_from)
# print self.mMinOverlap, overlap, xcol_from, xcol_to, col_from, col_to
if overlap > self.mMinOverlap:
return map(str, (fragment.getScore(),
fragment.getLength(),
fragment.getNumGaps(),
alignlib.calculatePercentSimilarity( fragment ),
fragment.getRowFrom(), fragment.getRowTo(),
fragment.getColFrom(), fragment.getColTo(),
overlap, xcol_from, xcol_to,
(xcol_to - xcol_from) - (col_to - col_from)) )
return ("0",) * 12
def CheckResult(self, result, info1, info2):
"""check if result is ok. Check for each fragment, if it overlaps
with the domains to be tested and dump if ok. This simulates
psiblast.
"""
row_from, row_to = map(string.atoi, info1[1:3])
col_from, col_to = map(string.atoi, info2[1:3])
## check for overlap
for fragment in self.mFragments:
# print alignlib.writeAlignataTable( fragment, 8, 1)
xcol_from = Tools.MapRight(fragment, row_from)
xcol_to = Tools.MapLeft(fragment, row_to)
overlap = min(col_to, xcol_to) - max(col_from, xcol_from)
# print self.mMinOverlap, overlap, xcol_from, xcol_to, col_from, col_to
if overlap > self.mMinOverlap:
return map(str, (fragment.getScore(), fragment.getLength(),
fragment.getNumGaps(),
alignlib.calculatePercentSimilarity(fragment),
fragment.getRowFrom(), fragment.getRowTo(),
fragment.getColFrom(), fragment.getColTo(),
overlap, xcol_from, xcol_to,
(xcol_to - xcol_from) - (col_to - col_from)))
return ("0", ) * 12
def CheckResult(self, result, info1=None, info2=None):
"""check if result is ok. The function below returns everything.
return tuple of strings as result.
"""
if (result.getLength() > 0):
row_ali, col_ali = alignlib.writeAlignataCompressed(result)
return map(
str,
(result.getScore(), result.getLength(), result.getNumGaps(),
alignlib.calculatePercentSimilarity(result),
result.getRowFrom(), result.getRowTo(), row_ali,
result.getColFrom(), result.getColTo(), col_ali))
else:
return ("0", ) * 12
def CheckResult( self,
result,
info1 = None,
info2 = None):
"""check if result is ok. The function below returns everything.
return tuple of strings as result.
"""
if (result.getLength() > 0):
row_ali, col_ali = alignlib.writeAlignataCompressed( result )
return map(str, (result.getScore(),
result.getLength(),
result.getNumGaps(),
alignlib.calculatePercentSimilarity( result ),
result.getRowFrom(), result.getRowTo(), row_ali,
result.getColFrom(), result.getColTo(), col_ali ) )
else:
return ("0",) * 12
overlap += ( min(r.mGenomeTo, t.mGenomeTo) - max(r.mGenomeFrom, t.mGenomeFrom))
rr += 1
tt += 1
if overlap == 0:
continue
map_reference2target.clear()
row = alignlib.makeSequence(reference.mTranslation)
col = alignlib.makeSequence(target.mTranslation)
alignator.align( map_reference2target, row, col )
f = alignlib.AlignmentFormatEmissions( map_reference2target )
row_ali, col_ali = f.mRowAlignment, f.mColAlignment
pidentity = 100.0 * alignlib.calculatePercentIdentity( map_reference2target, row, col )
psimilarity = 100.0 * alignlib.calculatePercentSimilarity( map_reference2target )
union = max( reference.mSbjctGenomeTo, target.mSbjctGenomeTo) - \
min( reference.mSbjctGenomeFrom, target.mSbjctGenomeFrom )
inter = min( reference.mSbjctGenomeTo, target.mSbjctGenomeTo) - \
max( reference.mSbjctGenomeFrom, target.mSbjctGenomeFrom )
assignment_id += 1
print string.join( map(str, (
assignment_id,
reference.mPredictionId,
target.mPredictionId,
0, 0,
overlap,
"%5.2f" % (100.0 * float(overlap) / float(min(len(reference.mTranslation), len(target.mTranslation)) * 3)),
elif o in ( "-h", "--help" ):
print globals()["__doc__"]
sys.exit(0)
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL, param_gop, param_gep )
map_query2token = alignlib.makeAlignmentVector()
for line in sys.stdin:
if line[0] == "#": continue
query_token, sbjct_token, query_sequence, sbjct_sequence = string.split(line[:-1], "\t")
map_query2token.clear()
row = alignlib.makeSequence(query_sequence)
col = alignlib.makeSequence(sbjct_sequence)
alignator.align( map_query2token, row, col )
pidentity = 100.0 * alignlib.calculatePercentIdentity( map_query2token, row, col )
psimilarity = 100.0 * alignlib.calculatePercentSimilarity( map_query2token )
print string.join( map(str, (
query_token, sbjct_token,
map_query2token.getScore(),
alignlib.AlignmentFormatEmissions( map_query2token ),
pidentity,
psimilarity,
map_query2token.getNumGaps()) ), "\t" )
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.makeSequence(peptide_sequences[entry.mQueryToken])
sbjct_sequence = alignlib.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.rescoreAlignment( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence,
alignlib.makeScorer( query_sequence, sbjct_sequence ) )
percent_identity = alignlib.calculatePercentIdentity( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence ) * 100
percent_similarity = alignlib.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.makeAlignmentVector()
xquery_from = exon_from / 3
xquery_to = exon_to / 3
alignlib.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.AlignmentFormatExplicit( tmp_ali, query_sequence, sbjct_sequence ) ) )
exon_percent_identity = alignlib.calculatePercentIdentity( tmp_ali,
query_sequence,
sbjct_sequence ) * 100
exon_percent_similarity = alignlib.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.makeAlignmentVector()
xquery_from = max( ref_from / 3, exon_from / 3)
xquery_to = min(ref_to / 3, exon_to / 3)
alignlib.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.AlignmentFormatExplicit( tmp_ali, query_sequence, sbjct_sequence ) )
percent_identity = alignlib.calculatePercentIdentity( tmp_ali,
query_sequence,
sbjct_sequence ) * 100
percent_similarity = alignlib.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" )
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.rescoreAlignment( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence,
alignlib.makeScorer( query_sequence, sbjct_sequence ) )
percent_identity = alignlib.calculatePercentIdentity( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence ) * 100
percent_similarity = alignlib.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"
