def parse_alignment(filename):
if filename.endswith("aln"):
ali = read(filename, 'clustal')
else:
ali = read(filename, 'fasta')
proc = run(["RNAalifold", "--noPS", filename], capture_output=True, check=True, text=True)
structure = proc.stdout.split('\n')[1].split(' ')[0]
assert len(structure) == len(ali[0])
return ali, structure
def main():
alignment = read(sys.stdin, 'fasta')
remove_chars = np.asarray(list(sys.argv[1]))
length = alignment.get_alignment_length()
for start in range(length):
if contains_none(alignment[:, start], remove_chars):
break
for end in range(length - 1, -1, -1):
if contains_none(alignment[:, end], remove_chars):
break
out = alignment[:, start:end + 1]
write(out, sys.stdout, 'fasta')
def main():
alignment = read(sys.stdin, "fasta")
remove_chars = np.asarray(list(sys.argv[1]))
length = alignment.get_alignment_length()
print("Num sequences: %d" % len(alignment), file=sys.stderr)
print("Alignment length: %d" % length, file=sys.stderr)
keep_cols = []
for i in tqdm(range(length)):
if not contains_only(alignment[:, i], remove_chars):
keep_cols.append(i)
out = np.empty((len(alignment), len(keep_cols)), dtype="<U1")
for i, j in tqdm(enumerate(keep_cols), total=len(keep_cols)):
out[:, i] = np.array(list(alignment[:, j]))
print("Remaining columns: %d" % out.shape[1], file=sys.stderr)
for i, seq in enumerate(alignment):
print(">" + seq.id)
print("".join(out[i, :]))
def createFirstGuessReferenceFromReads(self):
#TODO: I should make this a commandline parameter. More = MSA takes longer. Less = worse reference
msaReadCount = 4
print ('I choose ' + str(msaReadCount) + ' random reads.'
+ '\nThese are aligned to form a rough initial consensus sequence. Here:'
+ '\n' + join(self.outputRootDirectory,'Initial_Reference')
+ '\nPerforming ClustalO Multiple Sequence Alignment Now...')
try:
# Load Reads from File
parsedReads = list(parse(self.readInput, self.readInputFormat))
referenceSequence = None
# Reference Directory
referenceDirectory = join(self.outputRootDirectory,'Initial_Reference')
if not isdir(referenceDirectory):
makedirs(referenceDirectory)
if (len(parsedReads) > msaReadCount):
# Select a subset of reads for Multiple SequneceAlignment. Randomly, i guess.
randomIndexes = list(range(0, len(parsedReads)))
shuffle(randomIndexes)
rawClustalReads = []
for i in range(0,msaReadCount):
rawClustalReads.append(parsedReads[randomIndexes[i]])
rawClustalReadsFilename = join(referenceDirectory, 'MSARaw.fasta')
rawClustalReadsFileWriter = createOutputFile(rawClustalReadsFilename)
write(rawClustalReads, rawClustalReadsFileWriter, 'fasta')
rawClustalReadsFileWriter.close()
#Perform Clustal MSA
clustalOAlignmentOutputFileName = join(referenceDirectory, 'clustalOAlignment.fasta')
clustalOCommandLine = ClustalOmegaCommandline(infile=rawClustalReadsFilename, outfile=clustalOAlignmentOutputFileName, verbose=True, auto=True, force=True, threads=int(self.numberThreads))
clustalOCommandLine()
# Calculate consensus
# A dumb consensus has lots of ambiguous nucleotides. We'll polish those out later.
alignmentType = 'fasta'
alignmentObject = read(clustalOAlignmentOutputFileName, alignmentType)
alignmentSummaryInfo = AlignInfo.SummaryInfo(alignmentObject)
dumbConsensus = alignmentSummaryInfo.dumb_consensus(threshold=.5)
referenceSequence = SeqRecord(Seq(str(dumbConsensus) , IUPAC.IUPACUnambiguousDNA),
id='Initial_Consensus',
description='Initial_Consensus')
# Else
else:
# Select the first read, use it as the reference. It's something.
#referenceSequence = parsedReads[0]
# You know what? we should just give up. There aren't enough reads to assemble.
#raise Exception('Not enough reads to continue.')
referenceSequence = SeqRecord(Seq('' , IUPAC.IUPACUnambiguousDNA),
id='Initial_Consensus',
description='Initial_Consensus')
#Write reference to file
self.referenceSequenceFileName = join(referenceDirectory, 'FirstGuessReference.fasta')
firstGuessRefFileWriter = createOutputFile(self.referenceSequenceFileName)
write([referenceSequence], firstGuessRefFileWriter, 'fasta')
firstGuessRefFileWriter.close()
return self.referenceSequenceFileName
print ('Done making initial consensus sequence.')
except Exception:
print ('Exception encountered in createFirstGuessReferenceFromReads()')
print (exc_info()[0])
print (exc_info()[1])
print (exc_info()[2])
raise