#!/usr/bin/env python
import argparse
# from libkuleshov.debug import keyboard
from libkuleshov.fastx import read_fasta
##############################################################################
parser = argparse.ArgumentParser()
parser.add_argument('--ref')
parser.add_argument('--genome')
args = parser.parse_args()
##############################################################################
ref_fasta = read_fasta(args.ref)
with open(args.genome, 'w') as genome:
for ctg, fasta in ref_fasta.items():
genome.write('%s\t%d\n' % (ctg, len(fasta)))
#!/usr/bin/env python
import argparse
# from libkuleshov.debug import keyboard
from libkuleshov.fastx import read_fasta
##############################################################################
parser = argparse.ArgumentParser()
parser.add_argument('--ref')
parser.add_argument('--genome')
args = parser.parse_args()
##############################################################################
ref_fasta = read_fasta(args.ref)
with open(args.genome, 'w') as genome:
for ctg, fasta in ref_fasta.items():
genome.write('%s\t%d\n' % (ctg, len(fasta)))
total = sum(w for c, w in choices)
r = random.uniform(0, total)
upto = 0
for c, w in choices:
if upto + w >= r:
return c
upto += w
print choices
assert False, "Shouldn't get here"
##############################################################################
random.seed(0)
parse_fn = lambda x: int(x[1:].strip().split('|')[1])
ctg_fasta = read_fasta(args.ref, parse=parse_fn)
genome_lengths = [sum([len(ctg_fasta[ctg]) for ctg in org_contigs]) for org_contigs in ctg_by_org.values()]
organisms = ctg_by_org.keys()
total_sequence = sum(genome_lengths)
num_reads = int(total_sequence * args.cov / args.len)
num_organisms = len(ctg_by_org.keys())
positions_covered = dict()
for o in organisms:
positions_covered[o] = dict()
for ctg in ctg_by_org[o]:
positions_covered[o][ctg] = set()
fasta = open(args.fasta, 'w')
