def gapCdsToProteins(proteinAlignment, extraDnaSeqs=None):
""" to replace proteinToCodonAlignment() """
protSeqDict = {}
for seqRecord in proteinAlignment:
protSeqDict[seqRecord.id] = seqRecord
dnaFasta = patric_api.getSequenceOfFeatures(protSeqDict.keys(), 'dna')
#if Debug:
# LOG.write("dnaFasta sample: %s\n"%dnaFasta[:100])
dnaSeqDict = SeqIO.to_dict(
SeqIO.parse(StringIO(dnaFasta),
"fasta",
alphabet=IUPAC.IUPACAmbiguousDNA()))
for seqId in protSeqDict:
if extraDnaSeqs and seqId in extraDnaSeqs:
dnaSeqDict[seqId] = extraDnaSeqs[seqId]
if Debug:
LOG.write("appending extra DNA seq %s\n" % seqId)
if set(dnaSeqDict.keys()) != set(protSeqDict.keys()):
raise Exception(
"Protein and DNA sets differ:\nProteins: %s\nDNA: %s\n" %
(", ".join(sorted(protSeqDict)), ", ".join(sorted(dnaSeqDict))))
dnaAlignFasta = StringIO()
prot_align_len = proteinAlignment.get_alignment_length()
for seqId in dnaSeqDict:
dnaSeq = dnaSeqDict[seqId].seq
if len(dnaSeq) < 3 * prot_align_len:
# this is to handle cases where protein exists but DNA does not
dnaSeq += '---' * (prot_align_len - len(dnaSeq))
protSeq = protSeqDict[seqId].seq
dnaAlignFasta.write(">" + seqId + "\n")
dnaSeqPos = 0
for protPos in range(0, len(protSeq)):
if protSeq[protPos] == '-':
codon = '---'
else:
# TODO: in future use a codon table to check correct matching
codon = str(dnaSeq[dnaSeqPos:dnaSeqPos + 3])
dnaSeqPos += 3
dnaAlignFasta.write(codon)
protPos += 1 # should now be equal to prot_align_len
if Debug:
LOG.write(
seqId +
" protPos={0}, dnaSeqPos={1}, orig_DNA_len={2}, orig_prot_len={3}\n"
.format(protPos, dnaSeqPos, len(dnaSeq), len(protSeq)))
if protPos < prot_align_len:
dnaAlignFasta.write(''.join("---" * (prot_align_len - protPos)))
LOG.write(
"padding short seq {0}, of {1} pos out to {2}, orig_DNA_len={3}, orig_prot_len={4}\n"
.format(seqId, protPos, prot_align_len, len(dnaSeq),
len(protSeq)))
dnaAlignFasta.write("\n")
dnaAlignFasta_text = dnaAlignFasta.getvalue()
retval = AlignIO.read(StringIO(dnaAlignFasta_text), 'fasta')
return retval
proteinAlignments = {}
proteinAlignmentStats = {}
alignmentScore = {}
alignedTaxa = set()
protein_alignment_time = time()
for homologId in singleCopyHomologs:
try:
LOG.write("aligning {}\n".format(homologId))
geneIdSet = set()
for genome in homologMatrix[homologId]:
for proteinId in homologMatrix[homologId][genome]:
if not "undefined" in proteinId:
geneIdSet.add(proteinId)
#geneIdSet.update(set(homologMatrix[homologId][genome]))
proteinFasta = patric_api.getSequenceOfFeatures(geneIdSet, 'protein')
# replace bad characters for good while it is still text (e.g., 'J' to 'X')
lines = proteinFasta.split("\n")
for i in range(len(lines)):
if not lines[i].startswith(">"):
lines[i] = lines[i].replace("J", "X")
proteinFasta = "\n".join(lines)
seqRecords = SeqIO.parse(StringIO(proteinFasta),
"fasta",
alphabet=IUPAC.extended_protein)
proteinSeqDict = SeqIO.to_dict(seqRecords)
for genomeId in homologMatrix[homologId]:
for geneId in homologMatrix[homologId][genomeId]:
if genomeId == genomeObject_genomeId:
def proteinToCodonAlignment(proteinAlignment, extraDnaSeqs=None):
protSeqDict = {}
for seqRecord in proteinAlignment:
protSeqDict[seqRecord.id] = seqRecord
dnaFasta = patric_api.getSequenceOfFeatures(protSeqDict.keys(), 'dna')
#if Debug:
# LOG.write("dnaFasta sample: %s\n"%dnaFasta[:100])
dnaSeqDict = SeqIO.to_dict(
SeqIO.parse(StringIO(dnaFasta),
"fasta",
alphabet=IUPAC.IUPACAmbiguousDNA()))
for seqId in protSeqDict:
if extraDnaSeqs and seqId in extraDnaSeqs:
dnaSeqDict[seqId] = extraDnaSeqs[seqId]
if Debug:
LOG.write("appending extra DNA seq %s\n" % seqId)
if set(dnaSeqDict.keys()) != set(protSeqDict.keys()):
raise Exception(
"Protein and DNA sets differ:\nProteins: %s\nDNA: %s\n" %
(", ".join(sorted(protSeqDict)), ", ".join(sorted(dnaSeqDict))))
for seqId in dnaSeqDict:
if not len(dnaSeqDict[seqId].seq):
#del(dnaSeqDict[seqId])
LOG.write("warning: seqId %s length of dna was zero\n" % seqId)
dnaSeqRecords = []
for proteinSeq in proteinAlignment:
dnaSeqRecords.append(dnaSeqDict[proteinSeq.id])
if Debug:
LOG.write("dna seqs has %d seqs\n" % (len(dnaSeqRecords)))
#LOG.write("DNA seq ids: %s\n"%(", ".join(sorted(dnaSeqDict))))
#LOG.write("pro seq ids: %s\n"%(", ".join(sorted(protSeqDict))))
#LOG.write("first two aligned DNA seqs:\n")
#SeqIO.write(dnaSeqRecords[:2], LOG, "fasta")
#LOG.flush()
"""
# now check length of protein vs dna sequences, extend dna if needed to make match in numbers of codons
for i, protRec in enumerate(proteinAlignment):
protSeq = str(protRec.seq)
protSeq.replace('-','')
protLen = len(protSeq)
if len(dnaSeqs[i].seq) < protLen*3:
shortfall = (protLen*3) - len(dnaSeqs[i].seq)
if Debug:
LOG.write("DNA seq for %s is too short for protein, shortfall = %d\n"%(protRec.id, shortfall))
# extend on both ends to be safe
dnaSeqs[i].seq = "N"*shortfall + dnaSeqs[i].seq + "N"*shortfall
"""
returnValue = None
#with warnings.catch_warnings():
#warnings.simplefilter('ignore', BiopythonWarning)
#try:
#ambiguous_nucleotide_values = {'K': 'GT', 'M': 'AC', 'N': 'ACGT', 'S': 'CG', 'R': 'AG', 'W': 'AT', 'Y': 'CT'}
#ambiguous_protein_values = {'X': 'ACDEFGHIKLMNOPQRSTVWY', 'J': 'IL', 'B': 'DN', 'Z': 'EQ'}
#ambiguous_codon_table = CodonTable.AmbiguousCodonTable(CodonTable.ambiguous_dna_by_name["Standard"], IUPAC.IUPACAmbiguousDNA(), ambiguous_nucleotide_values, IUPAC.protein, ambiguous_protein_values)
#returnValue = codonalign.build(pro_align=proteinAlignment, nucl_seqs=dnaSeqRecords, codon_table=ambiguous_codon_table, max_score=1000)
returnValue = codonalign.build(pro_align=proteinAlignment,
nucl_seqs=dnaSeqRecords,
max_score=1000)
for dnaSeq in returnValue:
proteinRecord = protSeqDict[dnaSeq.id]
if proteinRecord.annotations:
dnaSeq.annotations = proteinRecord.annotations.copy()
#except Exception as e:
# LOG.write("problem in codonalign, skipping\n%s\n"%str(e))
# raise(e)
return returnValue