def simulate_instance(args):
print 'Started modyfiyng genome'
if not os.path.exists(args.output_path):
os.makedirs(args.output_path)
# genome_path = args.genome
contig_path = os.path.join(args.output_path, 'ctgs.fa')
read1_path = args.read1
read2_path = args.read2
bam_path = os.path.join(args.output_path, 'mapped')
gff_path = os.path.join(args.output_path, 'true_error_pos.gff')
gff_file = open(gff_path,'w')
genome_seqs = ReadInContigseqs(open(args.genome, 'r'),10)
#contigs/scaffolds
gap = args.gapsize
error = args.error
chunk_size = 20000
modified_genome = {}
modified_chunks = []
for acc,seq in genome_seqs.iteritems():
if acc == 'sequence_0':
pos = 0
chunks = [seq[i:i+chunk_size] for i in range(0, len(seq), chunk_size)]
i=0
for sample in range(100):
N_s = 'N'* max(0,(gap + error))
cut_size = gap + max(0,-error)
modified_chunk = chunks[i][: len(chunks[i])-(cut_size)] + N_s
#print modified_chunk
modified_chunks.append(modified_chunk)
i+=1
#print len(modified_chunk)
pos += len(modified_chunk)
if (gap + error) > 0:
error_start = pos - len(N_s)
error_stop = pos # error is anywhere in the introduced gap (either contraction or expansion)
else:
error_start = pos
error_stop = pos + 1 # error is at a specific position where a contraction has occured
if error < 0:
to_GFF(gff_file, '{0}'.format(acc), 'TRUTH','FCD', error_start, error_stop, 1, '+', '.', 'Note=Error:Contraction {0}bp'.format(abs(error)))
else:
to_GFF(gff_file, '{0}'.format(acc), 'TRUTH','FCD', error_start, error_stop, 1, '+', '.', 'Note=Error:Expansion {0}bp'.format(abs(error)))
mod_seq = ''.join(modified_chunks)
if error < 0:
modified_genome['scf_gap{0}_errorsize_minus{1}'.format(gap,error)] = mod_seq
else:
modified_genome['scf_gap{0}_errorsize{1}'.format(gap,error)] = mod_seq
else:
modified_genome[acc] = seq
#print and map
ctgs = open(contig_path,'w')
for acc,seq in modified_genome.iteritems():
ctgs.write('>{0}\n{1}\n'.format(acc,seq))
ctgs.close()
ctgs = open(contig_path,'r')
print 'Started mapping'
align.bwa_mem(read1_path, read2_path, contig_path, bam_path, args)
def simulate_instance(args):
print 'Started modyfiyng genome'
if not os.path.exists(args.output_path):
os.makedirs(args.output_path)
# genome_path = args.genome
contig_path = os.path.join(args.output_path, 'ctgs.fa')
read1_path = args.read1
read2_path = args.read2
bam_path = os.path.join(args.output_path, 'mapped')
gff_path = os.path.join(args.output_path, 'true_error_pos.gff')
gff_file = open(gff_path, 'w')
genome_seqs = ReadInContigseqs(open(args.genome, 'r'), 10)
#contigs/scaffolds
gap = args.gapsize
error = args.error
chunk_size = 20000
modified_genome = {}
modified_chunks = []
for acc, seq in genome_seqs.iteritems():
if acc == 'sequence_0':
pos = 0
chunks = [
seq[i:i + chunk_size] for i in range(0, len(seq), chunk_size)
]
i = 0
for sample in range(100):
N_s = 'N' * max(0, (gap + error))
cut_size = gap + max(0, -error)
modified_chunk = chunks[i][:len(chunks[i]) - (cut_size)] + N_s
#print modified_chunk
modified_chunks.append(modified_chunk)
i += 1
#print len(modified_chunk)
pos += len(modified_chunk)
if (gap + error) > 0:
error_start = pos - len(N_s)
error_stop = pos # error is anywhere in the introduced gap (either contraction or expansion)
else:
error_start = pos
error_stop = pos + 1 # error is at a specific position where a contraction has occured
if error < 0:
to_GFF(gff_file, '{0}'.format(acc), 'TRUTH', 'FCD',
error_start, error_stop, 1, '+', '.',
'Note=Error:Contraction {0}bp'.format(abs(error)))
else:
to_GFF(gff_file, '{0}'.format(acc), 'TRUTH', 'FCD',
error_start, error_stop, 1, '+', '.',
'Note=Error:Expansion {0}bp'.format(abs(error)))
mod_seq = ''.join(modified_chunks)
if error < 0:
modified_genome['scf_gap{0}_errorsize_minus{1}'.format(
gap, error)] = mod_seq
else:
modified_genome['scf_gap{0}_errorsize{1}'.format(
gap, error)] = mod_seq
else:
modified_genome[acc] = seq
#print and map
ctgs = open(contig_path, 'w')
for acc, seq in modified_genome.iteritems():
ctgs.write('>{0}\n{1}\n'.format(acc, seq))
ctgs.close()
ctgs = open(contig_path, 'r')
print 'Started mapping'
align.bwa_mem(read1_path, read2_path, contig_path, bam_path, args)
def simulate_instance(args):
print 'Started simulating'
if not os.path.exists(args.output_path):
os.makedirs(args.output_path)
genome_path = os.path.join(args.output_path, 'genome.fa')
contig_path = os.path.join(args.output_path, 'ctgs.fa')
read1_path = os.path.join(args.output_path, 'reads1.fa')
read2_path = os.path.join(args.output_path, 'reads2.fa')
bam_path = os.path.join(args.output_path, 'mapped')
gff_path = os.path.join(args.output_path, 'true_error_pos.gff')
gff_file = open(gff_path,'w')
#genome
genomelen = args.burnin + ( (args.contiglen+args.gaplen)*(args.nrgaps + 1 ) + args.contiglen ) * (len(args.errorsize) + 1)
print genomelen
g = genome.Genome([0.25]*4,genomelen,'genome1')
g.genome()
print >> open(genome_path,'w'), g.genome_fasta_format()
#contigs/scaffolds
if args.scaffolds:
scafs = open(contig_path,'w')
scafs.write('>scf_burnin{0}\n{1}\n'.format(args.gaplen,g.sequence[0:args.burnin]))
scaffold = ''
pos = args.burnin
for error in args.errorsize:
scaffold_coord = 0
for i,x in enumerate(range(pos, pos + (args.nrgaps + 1)*(args.contiglen + args.gaplen ), args.contiglen + args.gaplen)):
#print 'pos:', x
if (args.gaplen + error) > 0:
if i < args.nrgaps:
scaffold += g.sequence[x:x+args.contiglen]+ 'N'* (args.gaplen + error)
scaffold_coord = len(scaffold)
error_start = scaffold_coord - (args.gaplen + error)
error_stop = scaffold_coord # error is anywhere in the introduced gap (either contraction or expansion)
else:
scaffold += g.sequence[x:x+args.contiglen]
else:
#scaffold += g.sequence[i*(args.gaplen + error) + x : x + args.contiglen + (i+1)*(args.gaplen + error)]
scaffold += g.sequence[x : x + args.contiglen + (args.gaplen + error)]
scaffold_coord = len(scaffold)
error_start = scaffold_coord
error_stop = scaffold_coord+1 # error is at a specific position where a contraction has occured
if error < 0 and i < args.nrgaps:
to_GFF(gff_file, 'scf_gap{1}_errorsize_minus{2}'.format(i+1, args.gaplen, abs(error)), 'TRUTH','FCD', error_start, error_stop, 1, '+', '.', 'Note=Error:Contraction {0}bp'.format(abs(error)))
elif error > 0 and i < args.nrgaps:
to_GFF(gff_file, 'scf_gap{1}_errorsize{2}'.format(i+1, args.gaplen, abs(error)), 'TRUTH','FCD', error_start, error_stop, 1, '+', '.', 'Note=Error:Expansion {0}bp'.format(abs(error)))
else:
pass
if error <0:
scafs.write('>scf_gap{1}_errorsize_minus{2}\n{3}\n'.format(i+1, args.gaplen, abs(error), scaffold))
else:
scafs.write('>scf_gap{1}_errorsize{2}\n{3}\n'.format(i+1, args.gaplen, error, scaffold))
scaffold = ''
pos = x + 2*args.contiglen
# dummy sequences to prevent bwa tor remove any of our scaffolds
# for i in range(10):
# dummy = genome.Genome([0.25]*4,10000,'z_dummy{0}'.format(i+1))
# dummy.genome()
# scafs.write('>z_dummy{0}\n{1}\n'.format(i+1, dummy.sequence))
else:
ctgs = open(contig_path,'w')
ctgs.write('>ctg0\n{0}\n'.format(g.sequence[0:args.burnin]))
for i,x in enumerate(range(args.burnin,genomelen,(args.contiglen + args.gaplen))):
ctgs.write('>ctg{0}\n{1}\n'.format(i+1,g.sequence[x:x+args.contiglen]))
#reads
if args.distr == 'normal':
lib = reads.DNAseq(args.read_length ,args.coverage, distribution=args.distr, mean=args.mean,stddev=args.sd)
lib.simulate_pe_reads(g)
elif args.distr == 'uniform':
lib = reads.DNAseq(args.read_length ,args.coverage, distribution=args.distr, min_size=args.min_size,max_size=args.max_size)
lib.simulate_pe_reads(g)
reads1 = open(read1_path,'w')
reads2 = open(read2_path,'w')
i=0
for read in lib.fasta_format():
if i%2==0:
reads1.write(read)
else:
reads2.write(read)
i+=1
print 'Started mapping'
#mapping
#align.map_paired_reads(read1_path, read2_path, contig_path, bam_path, args)
align.bwa_mem(read1_path, read2_path, contig_path, bam_path, args)
def simulate_instance(args):
print 'Started simulating'
if not os.path.exists(args.output_path):
os.makedirs(args.output_path)
genome_path = os.path.join(args.output_path, 'genome.fa')
contig_path = os.path.join(args.output_path, 'ctgs.fa')
read1_path = os.path.join(args.output_path, 'reads1.fa')
read2_path = os.path.join(args.output_path, 'reads2.fa')
bam_path = os.path.join(args.output_path, 'mapped')
gff_path = os.path.join(args.output_path, 'true_error_pos.gff')
gff_file = open(gff_path, 'w')
#genome
genomelen = args.burnin + (
(args.contiglen + args.gaplen) *
(args.nrgaps + 1) + args.contiglen) * (len(args.errorsize) + 1)
print genomelen
g = genome.Genome([0.25] * 4, genomelen, 'genome1')
g.genome()
print >> open(genome_path, 'w'), g.genome_fasta_format()
#contigs/scaffolds
if args.scaffolds:
scafs = open(contig_path, 'w')
scafs.write('>scf_burnin{0}\n{1}\n'.format(args.gaplen,
g.sequence[0:args.burnin]))
scaffold = ''
pos = args.burnin
for error in args.errorsize:
scaffold_coord = 0
for i, x in enumerate(
range(
pos, pos + (args.nrgaps + 1) *
(args.contiglen + args.gaplen),
args.contiglen + args.gaplen)):
#print 'pos:', x
if (args.gaplen + error) > 0:
if i < args.nrgaps:
scaffold += g.sequence[x:x + args.contiglen] + 'N' * (
args.gaplen + error)
scaffold_coord = len(scaffold)
error_start = scaffold_coord - (args.gaplen + error)
error_stop = scaffold_coord # error is anywhere in the introduced gap (either contraction or expansion)
else:
scaffold += g.sequence[x:x + args.contiglen]
else:
#scaffold += g.sequence[i*(args.gaplen + error) + x : x + args.contiglen + (i+1)*(args.gaplen + error)]
scaffold += g.sequence[x:x + args.contiglen +
(args.gaplen + error)]
scaffold_coord = len(scaffold)
error_start = scaffold_coord
error_stop = scaffold_coord + 1 # error is at a specific position where a contraction has occured
if error < 0 and i < args.nrgaps:
to_GFF(
gff_file, 'scf_gap{1}_errorsize_minus{2}'.format(
i + 1, args.gaplen, abs(error)), 'TRUTH', 'FCD',
error_start, error_stop, 1, '+', '.',
'Note=Error:Contraction {0}bp'.format(abs(error)))
elif error > 0 and i < args.nrgaps:
to_GFF(
gff_file, 'scf_gap{1}_errorsize{2}'.format(
i + 1, args.gaplen, abs(error)), 'TRUTH', 'FCD',
error_start, error_stop, 1, '+', '.',
'Note=Error:Expansion {0}bp'.format(abs(error)))
else:
pass
if error < 0:
scafs.write('>scf_gap{1}_errorsize_minus{2}\n{3}\n'.format(
i + 1, args.gaplen, abs(error), scaffold))
else:
scafs.write('>scf_gap{1}_errorsize{2}\n{3}\n'.format(
i + 1, args.gaplen, error, scaffold))
scaffold = ''
pos = x + 2 * args.contiglen
# dummy sequences to prevent bwa tor remove any of our scaffolds
# for i in range(10):
# dummy = genome.Genome([0.25]*4,10000,'z_dummy{0}'.format(i+1))
# dummy.genome()
# scafs.write('>z_dummy{0}\n{1}\n'.format(i+1, dummy.sequence))
else:
ctgs = open(contig_path, 'w')
ctgs.write('>ctg0\n{0}\n'.format(g.sequence[0:args.burnin]))
for i, x in enumerate(
range(args.burnin, genomelen, (args.contiglen + args.gaplen))):
ctgs.write('>ctg{0}\n{1}\n'.format(
i + 1, g.sequence[x:x + args.contiglen]))
#reads
if args.distr == 'normal':
lib = reads.DNAseq(args.read_length,
args.coverage,
distribution=args.distr,
mean=args.mean,
stddev=args.sd)
lib.simulate_pe_reads(g)
elif args.distr == 'uniform':
lib = reads.DNAseq(args.read_length,
args.coverage,
distribution=args.distr,
min_size=args.min_size,
max_size=args.max_size)
lib.simulate_pe_reads(g)
reads1 = open(read1_path, 'w')
reads2 = open(read2_path, 'w')
i = 0
for read in lib.fasta_format():
if i % 2 == 0:
reads1.write(read)
else:
reads2.write(read)
i += 1
print 'Started mapping'
#mapping
#align.map_paired_reads(read1_path, read2_path, contig_path, bam_path, args)
align.bwa_mem(read1_path, read2_path, contig_path, bam_path, args)
def simulate_instance(args):
#print 'Started simulating'
if not os.path.exists(args.output_path):
os.makedirs(args.output_path)
if not args.contigs:
genome_path = os.path.join(args.output_path, 'genome.fa')
contig_path = os.path.join(args.output_path, 'ctgs.fa')
else:
genome_path = args.genome
contig_path = args.contigs
read1_path = os.path.join(args.output_path, 'reads1.fa')
read2_path = os.path.join(args.output_path, 'reads2.fa')
bam_path = os.path.join(args.output_path, 'mapped')
if not args.contigs:
#genome
#print args.genomelen
g = genome.Genome([0.25]*4,args.genomelen,'genome1')
g.genome()
print >> open(genome_path,'w'), g.genome_fasta_format()
#contigs
ctgs = open(contig_path,'w')
ctg_list = [x for x in contigs.generate_contigs(g.sequence,args.min_contig, args.max_contig, 0,3000)]
random.shuffle( ctg_list )
for ctg in ctg_list:
ctgs.write(ctg)
else:
g = genome.Genome([0.25]*4,args.genomelen,'genome1')
#print genome_path, args.genomelen
longest_seq = 0
for acc,seq in fasta.fasta_iter(open(genome_path,'r')):
print acc, len(seq)
if len(seq) > longest_seq:
g.sequence = seq
g.accession = acc
longest_seq = len(seq)
print 'chosen:',g.accession
#ctgs.write('>ctg0\n{0}\n'.format(g.sequence[0:args.burnin]))
#for i,x in enumerate(range(args.burnin,args.genomelen,(args.contiglen + args.gaplen))):
# ctgs.write('>ctg{0}\n{1}\n'.format(i+1,g.sequence[x:x+args.contiglen]))
#reads
if args.distr == 'normal':
lib = reads.DNAseq(args.read_length ,args.coverage, distribution=args.distr, mean=args.mean,stddev=args.sd)
lib.simulate_pe_reads(g)
elif args.distr == 'uniform':
lib = reads.DNAseq(args.read_length ,args.coverage, distribution=args.distr, min_size=args.min_size,max_size=args.max_size)
lib.simulate_pe_reads(g)
elif args.distr == 'mix':
lib_part1 = reads.DNAseq(args.read_length ,args.coverage/2, distribution='normal', mean=args.mean,stddev=args.sd)
lib_part1.simulate_pe_reads(g)
lib_part2 = reads.DNAseq(args.read_length ,args.coverage/2, distribution='uniform', min_size=(args.mean - 4*args.sd),max_size=(args.mean + 4*args.sd))
lib_part2.simulate_pe_reads(g)
# concatenate the reads from each distribution
lib = reads.DNAseq(args.read_length ,args.coverage, distribution=args.distr, mean=args.mean,stddev=args.sd)
lib.reads = lib_part1.reads + lib_part2.reads
reads1 = open(read1_path,'w')
reads2 = open(read2_path,'w')
i=0
for read in lib.fasta_format():
if i%2==0:
reads1.write(read)
else:
reads2.write(read)
i+=1
#print 'Started mapping'
#mapping
#align.map_paired_reads(read1_path, read2_path, contig_path, bam_path, args)
align.bwa_mem(read1_path, read2_path, genome_path, bam_path, args)