def multi_align_samples(self, retree=1):
# store here a dict, {sample_name: [sequence_id1, sequence_id2, ...]}
# because in Python3 OrderedDict does not have iteritems(), it simply has items()
if hasattr(self.genomeFastas, "iteritems"):
genomeKVIterator = self.genomeFastas.iteritems()
else:
genomeKVIterator = self.genomeFastas.items()
for sampleName, fastaFile in genomeKVIterator:
with util.file.open_or_gzopen(fastaFile, 'r') as inf:
for seq in Bio.SeqIO.parse(inf, 'fasta'):
self.sequence_order.setdefault(sampleName, default=[])
self.sequence_order[sampleName].append(seq.id)
inputFastas = []
inputFastas.append(self.ref)
inputFastas.extend(self.genomeFastas.values())
transposedFiles = interhost.transposeChromosomeFiles(inputFastas)
# since the FASTA files are
for idx, filePath in enumerate(transposedFiles):
outFile = util.file.mkstempfname('.fasta')
outFilePath = os.path.dirname(outFile)
alignedOutFile = tools.mafft.MafftTool().execute(
inFastas=[os.path.abspath(filePath)],
outFile=os.path.join(outFilePath,
"{}{}.fasta".format("aligned", idx)),
localpair=False,
globalpair=True,
preservecase=True,
reorder=None,
gapOpeningPenalty=None,
offset=None,
verbose=False,
outputAsClustal=None,
maxiters=1000,
threads=-1,
retree=retree)
self.alignedFastas.append(alignedOutFile)
def multi_align_samples(self, retree=1):
# store here a dict, {sample_name: [sequence_id1, sequence_id2, ...]}
# because in Python3 OrderedDict does not have iteritems(), it simply has items()
if hasattr(self.genomeFastas, "iteritems"):
genomeKVIterator = self.genomeFastas.iteritems()
else:
genomeKVIterator = self.genomeFastas.items()
for sampleName, fastaFile in genomeKVIterator:
with util.file.open_or_gzopen(fastaFile, 'r') as inf:
for seq in Bio.SeqIO.parse(inf, 'fasta'):
self.sequence_order.setdefault(sampleName, default=[])
self.sequence_order[sampleName].append(seq.id)
inputFastas = []
inputFastas.append(self.ref)
inputFastas.extend(self.genomeFastas.values())
transposedFiles = interhost.transposeChromosomeFiles(inputFastas)
# since the FASTA files are
for idx, filePath in enumerate(transposedFiles):
outFile = util.file.mkstempfname('.fasta')
outFilePath = os.path.dirname(outFile)
alignedOutFile = tools.mafft.MafftTool().execute(
inFastas=[os.path.abspath(filePath)],
outFile=os.path.join(outFilePath, "{}{}.fasta".format("aligned", idx)),
localpair=False,
globalpair=True,
preservecase=True,
reorder=None,
gapOpeningPenalty=None,
offset=None,
verbose=False,
outputAsClustal=None,
maxiters=1000,
threads=-1,
retree=retree)
self.alignedFastas.append(alignedOutFile)
def alignment_summary(inFastaFileOne, inFastaFileTwo, outfileName=None, printCounts=False):
""" Write or print pairwise alignment summary information for sequences in two FASTA
files, including SNPs, ambiguous bases, and indels.
"""
gap = '-'
ambiguous = 'N'
aligner = tools.muscle.MuscleTool()
per_chr_fastas = interhost.transposeChromosomeFiles([inFastaFileOne, inFastaFileTwo])
results = OrderedDict()
results["same_unambig"] = 0
results["snp_unambig"] = 0
results["indel_unambig"] = 0
results["indel_ambig"] = 0
results["ambig_one"] = 0
results["ambig_two"] = 0
results["ambig_both"] = 0
results["unambig_both"] = 0
for chr_fasta in per_chr_fastas:
same_unambig = 0
snp_unambig = 0
indel_unambig = 0
indel_ambig = 0
ambig_one = 0
ambig_two = 0
ambig_both = 0
unambig_both = 0
alignOutFileName = util.file.mkstempfname('.fasta')
aligner.execute(chr_fasta, alignOutFileName, fmt="clw")
with open(alignOutFileName, "r") as f:
alignment = Bio.AlignIO.read(f, "clustal")
for col_idx in range(0, alignment.get_alignment_length()):
col = alignment[:, col_idx]
c1 = col[0]
c2 = col[1]
if (c1 in ambiguous
and c2 in ambiguous):
ambig_both +=1
elif c1 in ambiguous:
ambig_one += 1
elif c2 in ambiguous:
ambig_two += 1
if (c1 in IUPACUnambiguousDNA().letters
and c2 in IUPACUnambiguousDNA().letters):
unambig_both += 1
if c1 == c2:
same_unambig += 1
else:
snp_unambig += 1
if ((c1 == gap and
c2 in IUPACUnambiguousDNA().letters) or
(c2 == gap and
c1 in IUPACUnambiguousDNA().letters)):
indel_unambig += 1
if ((c1 == gap and
c2 in ambiguous) or
(c2 == gap and
c1 in ambiguous)):
indel_ambig += 1
if printCounts:
print("Counts for this segment/chromosome:")
print("same_unambig ", same_unambig)
print("snp_unambig ", snp_unambig)
print("indel_unambig", indel_unambig)
print("indel_ambig ", indel_ambig)
print("ambig_one ", ambig_one)
print("ambig_two ", ambig_two)
print("ambig_both ", ambig_both)
print("unambig_both ", unambig_both)
results["same_unambig"] += same_unambig
results["snp_unambig"] += snp_unambig
results["indel_unambig"] += indel_unambig
results["indel_ambig"] += indel_ambig
results["ambig_one"] += ambig_one
results["ambig_two"] += ambig_two
results["ambig_both"] += ambig_both
results["unambig_both"] += unambig_both
if printCounts:
print("\nCounts for this sample:")
print("same_unambig ", results["same_unambig"])
print("snp_unambig ", results["snp_unambig"])
print("indel_unambig", results["indel_unambig"])
print("indel_ambig ", results["indel_ambig"])
print("ambig_one ", results["ambig_one"])
print("ambig_two ", results["ambig_two"])
print("ambig_both ", results["ambig_both"])
print("unambig_both ", results["unambig_both"])
if outfileName:
with open(outfileName, "wt") as of:
csvout = csv.writer(of, delimiter='\t')
csvout.writerow(list(results.keys()))
csvout.writerow(list(results.values()))
def alignment_summary(inFastaFileOne,
inFastaFileTwo,
outfileName=None,
printCounts=False):
""" Write or print pairwise alignment summary information for sequences in two FASTA
files, including SNPs, ambiguous bases, and indels.
"""
gap = '-'
ambiguous = 'N'
aligner = tools.muscle.MuscleTool()
per_chr_fastas = interhost.transposeChromosomeFiles(
[inFastaFileOne, inFastaFileTwo])
results = OrderedDict()
results["same_unambig"] = 0
results["snp_unambig"] = 0
results["indel_unambig"] = 0
results["indel_ambig"] = 0
results["ambig_one"] = 0
results["ambig_two"] = 0
results["ambig_both"] = 0
results["unambig_both"] = 0
for chr_fasta in per_chr_fastas:
same_unambig = 0
snp_unambig = 0
indel_unambig = 0
indel_ambig = 0
ambig_one = 0
ambig_two = 0
ambig_both = 0
unambig_both = 0
alignOutFileName = util.file.mkstempfname('.fasta')
aligner.execute(chr_fasta, alignOutFileName, fmt="clw")
with open(alignOutFileName, "r") as f:
alignment = Bio.AlignIO.read(f, "clustal")
for col_idx in range(0, alignment.get_alignment_length()):
col = alignment[:, col_idx]
c1 = col[0]
c2 = col[1]
if (c1 in ambiguous and c2 in ambiguous):
ambig_both += 1
elif c1 in ambiguous:
ambig_one += 1
elif c2 in ambiguous:
ambig_two += 1
if (c1 in IUPACUnambiguousDNA().letters
and c2 in IUPACUnambiguousDNA().letters):
unambig_both += 1
if c1 == c2:
same_unambig += 1
else:
snp_unambig += 1
if ((c1 == gap and c2 in IUPACUnambiguousDNA().letters) or
(c2 == gap and c1 in IUPACUnambiguousDNA().letters)):
indel_unambig += 1
if ((c1 == gap and c2 in ambiguous)
or (c2 == gap and c1 in ambiguous)):
indel_ambig += 1
if printCounts:
print("Counts for this segment/chromosome:")
print("same_unambig ", same_unambig)
print("snp_unambig ", snp_unambig)
print("indel_unambig", indel_unambig)
print("indel_ambig ", indel_ambig)
print("ambig_one ", ambig_one)
print("ambig_two ", ambig_two)
print("ambig_both ", ambig_both)
print("unambig_both ", unambig_both)
results["same_unambig"] += same_unambig
results["snp_unambig"] += snp_unambig
results["indel_unambig"] += indel_unambig
results["indel_ambig"] += indel_ambig
results["ambig_one"] += ambig_one
results["ambig_two"] += ambig_two
results["ambig_both"] += ambig_both
results["unambig_both"] += unambig_both
if printCounts:
print("\nCounts for this sample:")
print("same_unambig ", results["same_unambig"])
print("snp_unambig ", results["snp_unambig"])
print("indel_unambig", results["indel_unambig"])
print("indel_ambig ", results["indel_ambig"])
print("ambig_one ", results["ambig_one"])
print("ambig_two ", results["ambig_two"])
print("ambig_both ", results["ambig_both"])
print("unambig_both ", results["unambig_both"])
if outfileName:
with open(outfileName, "wt") as of:
csvout = csv.writer(of, delimiter='\t')
csvout.writerow(list(results.keys()))
csvout.writerow(list(results.values()))