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 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()
