def Generate(input, output, numins, numdel):
reference = list(input)
result = "".join([ch.seq for ch in reference])
l = sum([len(ch) for ch in reference])
ins = GroupByChrom(GenerateInsertions(numins, result), reference)
d = GroupByChrom(GenerateDeletions(numdel, result), reference)
for ch_ins, ch_d, chrom in itertools.izip(ins, d, reference):
sys.stdout.write("Chromosome " + chrom.id + "\n")
rec = SeqIO.SeqRecord(Apply(chrom.seq, ch_ins, ch_d), chrom.id)
SeqIO.write(rec, output, "fasta")
def collect_contigs(dataset, output_dir, output_base, format):
output = open(output_base + "." + format, "w")
for barcode in dataset:
file = os.path.join(output_dir, barcode.id, "truseq_long_reads." + format)
if os.path.exists(file):
contigs = SeqIO.parse(open(file), format)
for contig in contigs:
contig.id = barcode.id + "-" + contig.id
SeqIO.write(contig, output, format)
output.close()
def PrintResults(recs, reference, references_file, coordinates_file):
aln = open(coordinates_file, "w")
fasta = open(references_file, "w")
for rec in recs:
aln.write(str(rec) + "\n")
sequence = reference[rec.rname][rec.left:rec.right]
rec_id = str(rec.rname) + "_(" + str(rec.left) + "-" + str(rec.right)+")"
SeqIO.write(SeqIO.SeqRecord(sequence, rec_id), fasta, "fasta")
aln.close()
fasta.close()
def PrintResults(recs, reference, references_file, coordinates_file):
aln = open(coordinates_file, "w")
fasta = open(references_file, "w")
for rec in recs:
aln.write(str(rec) + "\n")
sequence = reference[rec.rname][rec.left:rec.right]
rec_id = str(rec.rname) + "_(" + str(rec.left) + "-" + str(
rec.right) + ")"
SeqIO.write(SeqIO.SeqRecord(sequence, rec_id), fasta, "fasta")
aln.close()
fasta.close()
def collect_contigs(dataset, barcodes_dir, output_base, format):
output = open(output_base + "." + format, "w")
for barcode in dataset:
file = os.path.join(barcodes_dir, barcode.id,
"truseq_long_reads." + format)
if os.path.exists(file):
contigs = SeqIO.parse(open(file), format)
for contig in contigs:
contig.id = barcode.id + "-" + contig.id
SeqIO.write(contig, output, format)
output.close()
def OutputBroken(self, output_file):
output = open(output_file, "w")
for contig in self.contigs:
for subcontig in self.Break(contig):
SeqIO.write(subcontig, output, "fasta")
output.close()
def write(self, rec):
SeqIO.write(rec, self.handlers[self.current_handler], "fastq")
self.current_handler = 1 - self.current_handler
self.count += 1
def OutputResults(output_file, format, result):
output = open(output_file + "." + format, "w")
for contig in result:
SeqIO.write(contig, output, format)
output.close()
def OutputResults(output_file, format, result):
output = open(output_file + "." + format, "w")
for contig in result:
SeqIO.write(contig, output, format)
output.close()
