def matchtrans(dnaseqs, pepseqs, gapin, verbose, mtx, allinternal,
readthroughstop):
dnaref = {}
dnaref_extra = {}
result = {}
# NOTICE: We need the handle the situation where more than one DNA
# sequence translates to the same peptide sequence.
#
# ASSUMPTION: Identical peptide sequences will align exactly the same
# way.
#
#
# EXAMPLE:
#
# dnaSeq17 -> pepSeq17
# dnaSeq32 -> pepSeq32
#
# *) dnaSeq17 and dnaSeq32 differs by a few nucleotides
#
# *) pepSeq17 and pepSeq32 are exactly the same
#
# Given the assmuption mentioned above, it does NOT
# matter if dnaSeq17 gets paired with pepSeq32
for key in dnaseqs.keys():
dna, note = dnaseqs[key]
dna = degap(dna, gapin)
newpep = mod_translate.translate(dna, mtx, not allinternal,
readthroughstop)
# Strip terminal stop-codon
if newpep.endswith("*"):
newpep = newpep[:-1]
if verbose > 2:
warn("DNA sequence " + key + " translated to:\n" + newpep)
if dnaref.has_key(newpep):
dnaref_extra[key] = newpep
else:
dnaref[newpep] = key
for key in pepseqs.keys():
pep, note = pepseqs[key]
pep = degap(pep, gapin).upper()
# Strip terminal stop-codon
if pep.endswith("*"):
pep = pep[:-1]
if verbose > 2:
warn("Pep sequence " + key + " degapped: \n" + pep)
if dnaref.has_key(pep):
result[key] = dnaref.pop(pep)
else:
for dnakey in dnaref_extra.keys():
if pep == dnaref_extra[dnakey]:
result[key] = dnakey
dnaref_extra.pop(dnakey)
break
return result
def revtrans(dnaseqs, pepseqs, crossref, gapin, gapout, verbose):
if verbose:
warn("gapin: '" + gapin + "'")
warn("gapout: '" + gapout + "'")
newdnaseqs = {}
error = 0
for key in pepseqs.keys():
try:
# Find the corresponding sequences
dna, pep, newdna = "", "", "" # Just in the case of an exception
if not key in crossref.keys():
warn("No cross-reference, skipping peptide sequence " + key)
continue
# print key,crossref[key]
dna, noted = dnaseqs[crossref[key]]
# dnaName = d_dnames[dna]
dnaName = crossref[key]
#print dna
dna = degap(dna, gapin)
pep, notep = pepseqs[key]
newdna = ""
dnap = 0
# +++++++ Start Modifications +++++++
newpep = ""
degapped = degap(pep, gapin)
dnap = -3 * initialgaps(
pep, gapin) # correct start if pep starts with gap characters
newpep = mod_translate.translate(dna, None, True, False)
# Strip terminal stop-codon
if newpep.endswith("*"):
newpep = newpep[:-1]
offset = string.find(newpep,
degapped) # offset start of rev translation
if offset < 0:
warn("Could not match pep:" + key)
dnap = dnap + 3 * offset
# +++++++ End Modifications +++++++
# Do the reverse translation for this seq
l_dna = []
for i in range(0, len(pep)):
c = pep[i]
if c in gapin:
l_dna.append(gapout * 3)
else:
# Extract codon - keep case from the amino acid
codon = dna[dnap:dnap + 3]
if c.isupper():
codon = codon.upper()
else:
codon = codon.lower()
l_dna.append(codon)
dnap = dnap + 3
# Everything's cool - add the new seq to the result
newdna = string.join(l_dna, "")
# newdnaseqs[key] = (newdna,noted)
newdnaseqs[dnaName] = (newdna, noted)
except:
if verbose:
warn("Error rev-translating seq:" + key)
warn("\nLen dna:" + str(len(dna)) + " pep:" + str(len(pep)) +
" newdna:" + str(len(newdna)) + "\n")
error = error + 1
return (newdnaseqs, error)
def matchtrans(dnaseqs,pepseqs,gapin,verbose,mtx,allinternal,readthroughstop):
dnaref = {}
dnaref_extra = {}
result = {}
# NOTICE: We need the handle the situation where more than one DNA
# sequence translates to the same peptide sequence.
#
# ASSUMPTION: Identical peptide sequences will align exactly the same
# way.
#
#
# EXAMPLE:
#
# dnaSeq17 -> pepSeq17
# dnaSeq32 -> pepSeq32
#
# *) dnaSeq17 and dnaSeq32 differs by a few nucleotides
#
# *) pepSeq17 and pepSeq32 are exactly the same
#
# Given the assmuption mentioned above, it does NOT
# matter if dnaSeq17 gets paired with pepSeq32
for key in dnaseqs.keys():
dna,note = dnaseqs[key]
dna = degap(dna,gapin)
newpep = mod_translate.translate(dna,mtx,not allinternal,readthroughstop)
# Strip terminal stop-codon
if newpep.endswith("*"):
newpep = newpep[:-1]
if verbose > 2:
warn("DNA sequence "+key+" translated to:\n"+newpep);
if dnaref.has_key(newpep):
dnaref_extra[key] = newpep
else:
dnaref[newpep] = key
for key in pepseqs.keys():
pep,note = pepseqs[key]
pep = degap(pep,gapin).upper()
# Strip terminal stop-codon
if pep.endswith("*"):
pep = pep[:-1]
if verbose > 2:
warn("Pep sequence "+key+" degapped: \n"+pep);
if dnaref.has_key(pep):
result[key] = dnaref.pop(pep)
else:
for dnakey in dnaref_extra.keys():
if pep == dnaref_extra[dnakey]:
result[key] = dnakey
dnaref_extra.pop(dnakey)
break
return result
qseq = dna elif rf == "2": qseq = dna[1:] elif rf == "3": qseq = dna[2:] elif rf == "-1": qseq = revCom(dna) elif rf == "-2": qseq = revCom(dna)[1:] elif rf == "-3": qseq = revCom(dna)[2:] else: qseq = dna # Do the actual translation pep = mod_translate.translate(qseq,mtx,not opt.allinternal,opt.readthroughstop) pa = mod_translate.annotate(qseq,mtx) # The annotation string may be longer that the peptide, if the -x more is not used pa = pa[:len(pep)] # Store translated sequence if echo_rf: cname = name+"_rframe"+rf else: cname = name data = ( cname,pep,pa,qseq ) d_collect[rf] = data # Do ORF finding?
qseq = dna elif rf == "2": qseq = dna[1:] elif rf == "3": qseq = dna[2:] elif rf == "-1": qseq = revCom(dna) elif rf == "-2": qseq = revCom(dna)[1:] elif rf == "-3": qseq = revCom(dna)[2:] else: qseq = dna # Do the actual translation pep = mod_translate.translate(qseq,mtx,not opt.allinternal,opt.readthroughstop) pa = mod_translate.annotate(qseq,mtx) # The annotation string may be longer that the peptide, if the -x more is not used pa = pa[:len(pep)] # Store translated sequence if echo_rf: cname = name+"_rframe"+rf else: cname = name data = ( cname,pep,pa,qseq ) d_collect[rf] = data # Do ORF finding?
continue
if arg == "--allinternal":
firstIsStart = False
continue
if arg == "-mtx":
mtxfn = argv[0]
argv = argv[1:]
continue
fn = arg
mtx = mod_translate.parseMatrixFile(mtxfn)
try:
seqs = mod_seqfiles.readfileauto(fn)
newseqs = {}
if not maxseqs: maxseqs = len(seqs.keys())
for key in seqs.keys()[0:maxseqs]:
seq, note = seqs[key]
newseqs[key] = mod_translate.translate(seq, mtx, firstIsStart,
readThroughStop), note
mod_seqfiles.writestream(sys.stdout, newseqs, "fasta", "P")
except Exception, e:
sys.stderr.write("Translation error: %s\n" % str(e))
sys.exit(1)
readThroughStop = True
continue
if arg == "--allinternal":
firstIsStart = False
continue
if arg == "-mtx":
mtxfn = argv[0]
argv = argv[1:]
continue
fn = arg
mtx = mod_translate.parseMatrixFile(mtxfn)
try:
seqs = mod_seqfiles.readfileauto(fn)
newseqs = {}
if not maxseqs: maxseqs = len(seqs.keys())
for key in seqs.keys()[0:maxseqs]:
seq, note = seqs[key]
newseqs[key] = mod_translate.translate(seq,mtx,firstIsStart,readThroughStop) , note
mod_seqfiles.writestream(sys.stdout,newseqs,"fasta","P")
except Exception, e:
sys.stderr.write("Translation error: %s\n" % str(e))
sys.exit(1)
