def getMapPeptide2Cds(peptide_sequence, cds_sequence, options):
"""get map between peptide sequence and cds sequence.
The returned alignment is in nucleotides.
"""
# remove whitespaces form protein sequence
p = re.sub(" ", "", peptide_sequence)
# remove gaps and whitespaces from cds
c = re.sub("[ .-]", "", cds_sequence)
w = Genomics.Protein2Wobble(p.upper())
if options.loglevel >= 6:
options.stdlog.write("# peptide original (%5i): %s\n" % (len(p), p))
options.stdlog.write("# cds original (%5i): %s\n" % (len(c), c))
options.stdlog.write("# wobble sequence (%5i): %s\n" % (len(w), w))
options.stdlog.flush()
seq_wobble = alignlib_lite.py_makeSequence(w)
seq_cds = alignlib_lite.py_makeSequence(c.upper())
seq_peptide = alignlib_lite.py_makeSequence(p)
map_p2c = alignlib_lite.py_makeAlignmentVector()
try:
AlignCodonBased(seq_wobble,
seq_cds,
seq_peptide,
map_p2c,
options=options)
except ValueError, msg:
raise ValueError("mapping error for sequence: %s" % (msg))
def getMapPeptide2Cds(peptide_sequence, cds_sequence, options):
"""get map between peptide sequence and cds sequence.
The returned alignment is in nucleotides.
"""
# remove whitespaces form protein sequence
p = re.sub(" ", "", peptide_sequence)
# remove gaps and whitespaces from cds
c = re.sub("[ .-]", "", cds_sequence)
w = Genomics.Protein2Wobble(p.upper())
if options.loglevel >= 6:
options.stdlog.write("# peptide original (%5i): %s\n" % (len(p), p))
options.stdlog.write("# cds original (%5i): %s\n" % (len(c), c))
options.stdlog.write("# wobble sequence (%5i): %s\n" % (len(w), w))
options.stdlog.flush()
seq_wobble = alignlib_lite.py_makeSequence(w)
seq_cds = alignlib_lite.py_makeSequence(c.upper())
seq_peptide = alignlib_lite.py_makeSequence(p)
map_p2c = alignlib_lite.py_makeAlignmentVector()
try:
AlignCodonBased(seq_wobble,
seq_cds,
seq_peptide,
map_p2c,
options=options)
except ValueError as msg:
raise ValueError("mapping error for sequence: %s" % (msg))
# if there are more than five frameshifts - do exhaustive alignment
max_gaps = 5
num_peptide_gaps = len(re.sub("[^-]", "", p))
ngaps = map_p2c.getNumGaps() - \
(num_peptide_gaps * 3) - abs(len(w) - len(c))
if options.loglevel >= 6:
options.stdlog.write(
"# alignment between wobble and cds: ngaps=%i, npeptide_gaps=%i\n"
% (ngaps, num_peptide_gaps))
printPrettyAlignment(seq_wobble, seq_cds, p, map_p2c, options)
if ngaps > max_gaps:
if options.loglevel >= 2:
options.stdlog.write(
"# too many gaps (%i>%i), realigning exhaustively.\n" %
(ngaps, max_gaps))
options.stdlog.flush()
full_map_p2c = alignlib_lite.py_makeAlignmentVector()
AlignExhaustive(seq_wobble, seq_cds, seq_peptide, full_map_p2c,
options)
if options.loglevel >= 6:
options.stdlog.write("# full alignment between wobble and cds:\n")
options.stdlog.flush()
printPrettyAlignment(seq_wobble, seq_cds, p, full_map_p2c, options)
map_p2c = full_map_p2c
# remove incomplete codons
x = 0
while x < len(p) * 3:
if (map_p2c.mapRowToCol(x) < 0 or map_p2c.mapRowToCol(x + 1) < 0
or map_p2c.mapRowToCol(x + 2) < 0):
map_p2c.removeRowRegion(x, x + 3)
x += 3
if map_p2c.getLength() == 0:
if options.loglevel >= 1:
options.stdlog.write("# WARNING: empty alignment\n")
if options.loglevel >= 6:
options.stdlog.write("# peptide original: %s\n" % p)
options.stdlog.write("# cds original : %s\n" % c)
options.stdlog.write("# wobble sequence : %s\n" % w)
raise ValueError("empty alignment")
assert (map_p2c.getRowTo() <= seq_wobble.getLength())
assert (map_p2c.getColTo() <= seq_cds.getLength())
return map_p2c
