def process_long_ccs_read_buffer(rbe,buffer,args):
#rbe = SimulationBasics.RandomBiallelicTranscriptomeEmitter()
#rbe.read_serialized(rbe_ser)
fq_prof_pacbio_ccs95 = default_pacbio_ccs95()
read1 = ''
zend = 0
for z in buffer:
[name,seq] = rbe.emit_long_read()
g = 'm150101_010101_11111_c111111111111111111_s1_p0/'+str(z)+'/ccs'
zend = z
read1 += "@"+g+"\n"
if args.no_errors:
read1 += seq+"\n"
read1 += "+\n"
read1 += len(seq)*'I'+"\n"
else:
seqperm = fq_prof_pacbio_ccs95.create_fastq_and_permute_sequence(seq)
read1 += seqperm['seq']+"\n"
read1 += "+\n"
read1 += seqperm['qual']+"\n"
return [read1,len(buffer),rbe.emissions_report]
def process_long_ccs_read_buffer(rbe, buffer, args):
#rbe = SimulationBasics.RandomBiallelicTranscriptomeEmitter()
#rbe.read_serialized(rbe_ser)
fq_prof_pacbio_ccs95 = default_pacbio_ccs95()
read1 = ''
zend = 0
for z in buffer:
[name, seq] = rbe.emit_long_read()
g = 'm150101_010101_11111_c111111111111111111_s1_p0/' + str(z) + '/ccs'
zend = z
read1 += "@" + g + "\n"
if args.no_errors:
read1 += seq + "\n"
read1 += "+\n"
read1 += len(seq) * 'I' + "\n"
else:
seqperm = fq_prof_pacbio_ccs95.create_fastq_and_permute_sequence(
seq)
read1 += seqperm['seq'] + "\n"
read1 += "+\n"
read1 += seqperm['qual'] + "\n"
return [read1, len(buffer), rbe.emissions_report]
def main():
parser = argparse.ArgumentParser(
description="Create a simulated RNA-seq dataset")
group0 = parser.add_mutually_exclusive_group(required=True)
group0.add_argument(
'--load_biallelic_transcriptome',
help=
"SERIALIZED BIALLELIC TRANSCRIOTOME EMITTER FILE to load up and use instead of all other file inputs"
)
group0.add_argument(
'--inputs',
nargs=3,
help="<reference_genome> <phased_VCF> <transcripts_genepred>")
#parser.add_argument('reference_genome',help="The reference genome.")
#parser.add_argument('phased_VCF',help="A phased VCF file. If you are simulating the genomes that step can make on of these for you.")
#parser.add_argument('transcripts_genepred',help="A genepred file describing the transcripts. Each transcript name must be unique.")
group = parser.add_mutually_exclusive_group()
group.add_argument('--uniform_expression',
action='store_true',
help="Uniform distribution of transcript expression")
group.add_argument(
'--isoform_expression',
help=
"The transcript expression in TSV format <Transcript name> tab <Expression>"
)
group.add_argument(
'--cufflinks_isoform_expression',
help=
"The expression of the isoforms or - for a uniform distribution of transcript expression"
)
group2 = parser.add_mutually_exclusive_group()
group2.add_argument(
'--ASE_identical',
type=float,
help=
"The ASE for the transcriptome, every isoform will have the same allele preference."
)
group2.add_argument('--ASE_isoform_random',
action='store_true',
help="The ASE will be random for every isoform.")
group2.add_argument(
'--ASE_locus_random',
action='store_true',
help="The ASE will be randomly assigned for each locus")
parser.add_argument('--short_read_count',
type=int,
default=10000,
help="INT number of short reads")
parser.add_argument('--short_read_length',
type=int,
default=101,
help="INT length of the short reads")
parser.add_argument('--long_read_ccs_count',
type=int,
default=4000,
help="INT default number of long reads")
parser.add_argument('--long_read_subread_count',
type=int,
default=4000,
help="INT default number of long reads")
parser.add_argument('--no_errors',
action='store_true',
help="Do not simulate errors in reads")
parser.add_argument('--threads',
type=int,
default=cpu_count(),
help="Number of threads defaults to cpu_count()")
parser.add_argument(
'--locus_by_gene_name',
action='store_true',
help="Faster than the complete calculation for overlapping loci.")
parser.add_argument(
'--seed',
type=int,
help=
"seed to make transcriptome and rho creation deterministic. Reads are still random, its just the transcriptome and rho that become determinisitic."
)
group3 = parser.add_mutually_exclusive_group(required=True)
group3.add_argument('--output', help="Directory name for output")
group3.add_argument(
'--save_biallelic_transcriptome',
help=
"FILENAME output the biallelic transcriptome used to this file and then exit"
)
parser.add_argument(
'--starting_read_multiplier',
type=int,
default=0,
help=
"Used if outputting different reads from object, and you want them number differently give each different set values 0, 1, 2, etc..."
)
args = parser.parse_args()
fq_prof_illumina = None
fq_prof_pacbio_ccs95 = None
fq_prof_pacbio_subreads = None
if not args.no_errors:
fq_prof_illumina = default_illumina()
fq_prof_pacbio_ccs95 = default_pacbio_ccs95()
fq_prof_pacbio_subreads = default_pacbio_subreads()
rbe = None
if not args.load_biallelic_transcriptome:
# we need to establish the emitter based on some known data
rbe = load_from_inputs(args)
else:
rbe = SimulationBasics.RandomBiallelicTranscriptomeEmitter()
inf = open(args.load_biallelic_transcriptome)
sline = inf.readline().rstrip()
inf.close()
rbe.read_serialized(sline)
if args.save_biallelic_transcriptome:
ofser = open(args.save_biallelic_transcriptome, 'w')
ofser.write(rbe.get_serialized())
ofser.close()
return #exiting here
# Lets prepare to output now
args.output = args.output.rstrip('/')
if not os.path.exists(args.output):
os.makedirs(args.output)
ofser = open(
args.output + "/RandomBiallelicTranscriptomeEmitter.serialized", 'w')
ofser.write(rbe.get_serialized())
ofser.close()
rbe.set_gaussian_fragmentation_default_hiseq()
#rbe_ser = rbe.get_serialized()
sys.stderr.write("Sequencing short reads\n")
global shand1
shand1 = gzip.open(args.output + "/SR_1.fq.gz", 'wb')
global shand2
shand2 = gzip.open(args.output + "/SR_2.fq.gz", 'wb')
z = 0
buffer_full_size = 5000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(args.short_read_count * args.starting_read_multiplier,
args.short_read_count *
(args.starting_read_multiplier + 1)):
z = i + 1
buffer.append(z)
if buffer_full_size <= len(buffer):
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_short_read_buffer,
args=(rbe, vals, args),
callback=write_short_reads)
else:
oval = process_short_read_buffer(rbe, vals, args)
write_short_reads(oval)
if len(buffer) > 0:
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_short_read_buffer,
args=(rbe, vals, args),
callback=write_short_reads)
else:
oval = process_short_read_buffer(rbe, vals, args)
write_short_reads(oval)
if args.threads > 1:
p.close()
p.join()
sys.stderr.write("\nFinished sequencing short reads\n")
shand1.close()
shand2.close()
global emissions_reports
for i in range(0, len(emissions_reports)):
emissions_reports[i] = emissions_reports[i].get()
sr_report = combine_reports(emissions_reports)
rbe.emissions_report = {} # initialize so we don't accidentally overwrite
# Now lets print out some of the emission details
of = open(args.output + "/SR_report.txt", 'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in sr_report:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" +
str(sr_report[name][0]) + "\t" + str(sr_report[name][1]) +
"\n")
else:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" + str(0) + "\t" +
str(0) + "\n")
of.close()
rbe.emissions_report = {}
emissions_reports = []
# Now lets create the long read set
rbe.set_gaussian_fragmentation_default_pacbio()
#rbe_ser = rbe.get_serialized()
sys.stderr.write("Sequencing long ccs reads\n")
shand1 = gzip.open(args.output + "/LR_ccs95.fq.gz", 'wb')
buffer_full_size = 500
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(args.starting_read_multiplier * args.long_read_ccs_count,
(args.starting_read_multiplier + 1) *
args.long_read_ccs_count):
z = i + 1
buffer.append(z)
if buffer_full_size <= len(buffer):
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_ccs_read_buffer,
args=(rbe, vals, args),
callback=write_long_reads)
else:
oval = process_long_ccs_read_buffer(rbe, vals, args)
write_long_reads(oval)
if len(buffer) > 0:
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_ccs_read_buffer,
args=(rbe, vals, args),
callback=write_long_reads)
else:
oval = process_long_ccs_read_buffer(rbe, vals, args)
write_long_reads(oval)
if args.threads > 1:
p.close()
p.join()
sys.stderr.write("\nFinished sequencing long reads\n")
shand1.close()
for i in range(0, len(emissions_reports)):
emissions_reports[i] = emissions_reports[i].get()
lr_ccs_report = combine_reports(emissions_reports)
rbe.emissions_report = {} # initialize so we don't accidentally overwrite
# Now lets print out some of the emission details
of = open(args.output + "/LR_ccs95_report.txt", 'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in lr_ccs_report:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" +
str(lr_ccs_report[name][0]) + "\t" +
str(lr_ccs_report[name][1]) + "\n")
else:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" + str(0) + "\t" +
str(0) + "\n")
of.close()
rbe.emissions_report = {}
emissions_reports = []
# Now lets create the long subread read set
rbe.set_gaussian_fragmentation_default_pacbio()
#rbe_ser = rbe.get_serialized()
sys.stderr.write("Sequencing long subreads\n")
shand1 = gzip.open(args.output + "/LR_subreads.fq.gz", 'wb')
buffer_full_size = 500
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(
args.long_read_subread_count * args.starting_read_multiplier,
(args.starting_read_multiplier + 1) * args.long_read_subread_count):
z = i + 1
buffer.append(z)
if buffer_full_size <= len(buffer):
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_sub_read_buffer,
args=(rbe, vals, args),
callback=write_long_reads)
else:
oval = process_long_sub_read_buffer(rbe, vals, args)
write_long_reads(oval)
if len(buffer) > 0:
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_sub_read_buffer,
args=(rbe, vals, args),
callback=write_long_reads)
else:
oval = process_long_sub_read_buffer(rbe, vals, args)
write_long_reads(oval)
if args.threads > 1:
p.close()
p.join()
sys.stderr.write("\nFinished sequencing long reads\n")
shand1.close()
for i in range(0, len(emissions_reports)):
emissions_reports[i] = emissions_reports[i].get()
lr_sub_report = combine_reports(emissions_reports)
rbe.emissions_report = {} # initialize so we don't accidentally overwrite
# Now lets print out some of the emission details
of = open(args.output + "/LR_subreads_report.txt", 'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in lr_sub_report:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" +
str(lr_sub_report[name][0]) + "\t" +
str(lr_sub_report[name][1]) + "\n")
else:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" + str(0) + "\t" +
str(0) + "\n")
of.close()
combo_report = combine_reports([sr_report, lr_ccs_report, lr_sub_report])
of = open(args.output + "/LR_SR_combo_report.txt", 'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in combo_report:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" +
str(combo_report[name][0]) + "\t" +
str(combo_report[name][1]) + "\n")
else:
of.write(name + "\t" + rbe.gene_names[name] + "\t" +
str(rbe.name2locus[name]) + "\t" + str(express) + "\t" +
str(rbe.transcriptome1_rho[name]) + "\t" + str(0) + "\t" +
str(0) + "\n")
of.close()
def main():
parser = argparse.ArgumentParser(
description="Create a simulated RNA-seq dataset")
parser.add_argument('reference_genome', help="The reference genome.")
parser.add_argument(
'transcripts_genepred',
help=
"A genepred file describing the transcripts. Each transcript name must be unique."
)
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('--uniform_expression',
action='store_true',
help="Uniform distribution of transcript expression")
group.add_argument(
'--isoform_expression',
help=
"The transcript expression in TSV format <Transcript name> tab <Expression>"
)
group.add_argument(
'--cufflinks_isoform_expression',
help=
"The expression of the isoforms or - for a uniform distribution of transcript expression"
)
group2 = parser.add_mutually_exclusive_group()
group2.add_argument('--long_reads_only', action='store_true')
group2.add_argument('--short_reads_only', action='store_true')
group2.add_argument('--output', help="Directory name for output")
parser.add_argument('--short_read_count',
type=int,
default=10000,
help="INT number of short reads")
parser.add_argument('--short_read_length',
type=int,
default=101,
help="INT length of the short reads")
parser.add_argument('--long_read_count',
type=int,
default=4000,
help="INT default number of long reads")
parser.add_argument('--no_errors', action='store_true')
parser.add_argument('--threads', type=int, default=1)
args = parser.parse_args()
if args.output:
args.output = args.output.rstrip('/')
fq_prof_pacbio_ccs95 = None
fq_prof_pacbio_subreads = None
fq_prof_illumina = None
if not args.no_errors:
fq_prof_pacbio_ccs95 = default_pacbio_ccs95()
fq_prof_pacbio_subreads = default_pacbio_subreads()
fq_prof_illumina = default_illumina()
ref = read_fasta_into_hash(args.reference_genome)
txn = Transcriptome()
txn.set_reference_genome_dictionary(ref)
with open(args.transcripts_genepred) as inf:
for line in inf:
if line[0] == '#': continue
txn.add_genepred_line(line.rstrip())
if args.isoform_expression:
sys.stderr.write("Reading expression from a TSV\n")
with open(args.isoform_expression) as inf:
line1 = inf.readline()
for line in inf:
f = line.rstrip().split("\t")
txn.add_expression(f[0], float(f[1]))
elif args.uniform_expression:
sys.stderr.write("Using uniform expression model\n")
elif args.cufflinks_isoform_expression:
sys.stderr.write("Using cufflinks expression\n")
with open(args.cufflinks_isoform_expression) as inf:
line1 = inf.readline()
for line in inf:
f = line.rstrip().split("\t")
txn.add_expression(f[0], float(f[9]))
sys.stderr.write("have transcriptome\n")
for n in txn.ref_hash.keys():
del txn.ref_hash[n]
rbe = SimulationBasics.RandomTranscriptomeEmitter(txn)
# Now we have the transcriptomes set
#Now our dataset is set up
if args.short_reads_only:
rbe.set_gaussian_fragmentation_default_hiseq()
for zi in range(0, args.short_read_count):
[name, seq] = rbe.emit_short_read(args.short_read_length)
if args.no_errors:
print "@SRSIM" + str(zi + 1)
print seq
print "+"
print 'I' * len(seq)
else:
l1perm = fq_prof_illumina.create_fastq_and_permute_sequence(
seq)
print "@SRSIM" + str(zi + 1)
print l1perm['seq']
print "+"
print l1perm['qual']
return
if args.long_reads_only:
rbe.set_gaussian_fragmentation_default_pacbio()
for zi in range(0, args.long_read_count):
[name, seq] = rbe.emit_long_read()
if args.no_errors:
g = 'm150101_010101_11111_c111111111111111111_s1_p0/' + str(
zi + 1) + '/ccs'
print "@" + g
print seq
print "+"
print 'I' * len(seq)
else:
g = 'm150101_010101_11111_c111111111111111111_s1_p0/' + str(
zi + 1) + '/ccs'
seqperm = fq_prof_pacbio_ccs95.create_fastq_and_permute_sequence(
seq)
print "@" + g
print seqperm['seq']
print "+"
print seqperm['qual']
return
if not os.path.exists(args.output):
os.makedirs(args.output)
rbe.set_gaussian_fragmentation_default_hiseq()
# Lets prepare to output now
sys.stderr.write("Sequencing short reads\n")
global left_handle
global right_handle
left_handle = gzip.open(args.output + "/SR_1.fq.gz", 'wb')
right_handle = gzip.open(args.output + "/SR_2.fq.gz", 'wb')
buffer_size = 10000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
z = 0
for i in range(0, args.short_read_count):
z = i + 1
if z % 1000 == 0: sys.stderr.write(str(z) + "\r")
buffer.append(z)
if len(buffer) >= buffer_size:
if args.threads <= 1:
v = process_short_read_buffer(buffer[:], rbe, args,
fq_prof_illumina)
do_short(v)
else:
p.apply_async(process_short_read_buffer,
args=(buffer[:], rbe, args, fq_prof_illumina),
callback=do_short)
buffer = []
if len(buffer) > 0:
if args.threads <= 1:
v = process_short_read_buffer(buffer[:], rbe, args,
fq_prof_illumina)
do_short(v)
else:
p.apply_async(process_short_read_buffer,
args=(buffer[:], rbe, args, fq_prof_illumina),
callback=do_short)
buffer = []
if args.threads > 1:
p.close()
p.join()
global greport
of = open(args.output + "/SR_report.txt", 'w')
for name in greport:
of.write("\t".join([str(x) for x in greport[name]]) + "\n")
of.close()
greport = {}
sys.stderr.write("\nFinished sequencing short reads\n")
left_handle.close()
right_handle.close()
# Now lets create the long read set
rbe.set_gaussian_fragmentation_default_pacbio()
sys.stderr.write("Sequencing ccs long reads\n")
global long_handle
long_handle = gzip.open(args.output + "/LR_ccs.fq.gz", 'wb')
buffer_size = 1000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
z = 0
for i in range(0, args.long_read_count):
z = i + 1
if z % 100 == 0: sys.stderr.write(str(z) + "\r")
buffer.append(z)
if len(buffer) >= buffer_size:
if args.threads <= 1:
v = process_long_reads(buffer[:], rbe, args,
fq_prof_pacbio_ccs95, 'ccs')
do_long(v)
else:
p.apply_async(process_long_reads,
args=(buffer[:], rbe, args, fq_prof_pacbio_ccs95,
'ccs'),
callback=do_long)
buffer = []
if len(buffer) > 0:
if args.threads <= 1:
v = process_long_reads(buffer[:], rbe, args, fq_prof_pacbio_ccs95,
'ccs')
do_long(v)
else:
p.apply_async(process_long_reads,
args=(buffer[:], rbe, args, fq_prof_pacbio_ccs95,
'ccs'),
callback=do_long)
buffer = []
if args.threads > 1:
p.close()
p.join()
long_handle.close()
of = open(args.output + "/LR_ccs_report.txt", 'w')
for name in greport:
of.write("\t".join([str(x) for x in greport[name]]) + "\n")
of.close()
greport = {}
sys.stderr.write("\nFinished sequencing ccs long reads\n")
sys.stderr.write("Sequencing long sub reads\n")
long_handle = gzip.open(args.output + "/LR_sub.fq.gz", 'wb')
buffer_size = 1000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(z, z + args.long_read_count):
z = i + 1
if z % 100 == 0: sys.stderr.write(str(z) + "\r")
buffer.append(z)
if len(buffer) >= buffer_size:
if args.threads <= 1:
v = process_long_reads(buffer[:], rbe, args,
fq_prof_pacbio_subreads, 'sub')
do_long(v)
else:
p.apply_async(process_long_reads,
args=(buffer[:], rbe, args,
fq_prof_pacbio_subreads, 'sub'),
callback=do_long)
buffer = []
if len(buffer) > 0:
if args.threads <= 1:
v = process_long_reads(buffer[:], rbe, args,
fq_prof_pacbio_subreads, 'sub')
do_long(v)
else:
p.apply_async(process_long_reads,
args=(buffer[:], rbe, args, fq_prof_pacbio_subreads,
'sub'),
callback=do_long)
buffer = []
if args.threads > 1:
p.close()
p.join()
long_handle.close()
of = open(args.output + "/LR_sub_report.txt", 'w')
for name in greport:
of.write("\t".join([str(x) for x in greport[name]]) + "\n")
of.close()
greport = {}
sys.stderr.write("\nFinished sequencing long sub reads\n")
combo = {}
with open(args.output + "/SR_report.txt") as inf:
for line in inf:
f = line.rstrip().split("\t")
[name, express, left] = f
if name not in combo:
combo[name] = {}
combo[name]['express'] = express
combo[name]['left'] = 0
combo[name]['left'] += int(left)
with open(args.output + "/LR_ccs_report.txt") as inf:
for line in inf:
f = line.rstrip().split("\t")
[name, express, left] = f
if name not in combo:
combo[name] = {}
combo[name]['express'] = express
combo[name]['left'] = 0
combo[name]['left'] += int(left)
with open(args.output + "/LR_sub_report.txt") as inf:
for line in inf:
f = line.rstrip().split("\t")
[name, express, left] = f
if name not in combo:
combo[name] = {}
combo[name]['express'] = express
combo[name]['left'] = 0
combo[name]['left'] += int(left)
of = open(args.output + "/LR_SR_combo_report.txt", 'w')
for name in sorted(combo):
of.write(name + "\t" + combo[name]['express'] + "\t" +
str(combo[name]['left']) + "\n")
of.close()
def main():
parser = argparse.ArgumentParser(description="Create a simulated RNA-seq dataset")
parser.add_argument('reference_genome',help="The reference genome.")
parser.add_argument('transcripts_genepred',help="A genepred file describing the transcripts. Each transcript name must be unique.")
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('--uniform_expression',action='store_true',help="Uniform distribution of transcript expression")
group.add_argument('--isoform_expression',help="The transcript expression in TSV format <Transcript name> tab <Expression>")
group.add_argument('--cufflinks_isoform_expression',help="The expression of the isoforms or - for a uniform distribution of transcript expression")
group2 = parser.add_mutually_exclusive_group()
group2.add_argument('--long_reads_only',action='store_true')
group2.add_argument('--short_reads_only',action='store_true')
group2.add_argument('--output',help="Directory name for output")
parser.add_argument('--short_read_count',type=int,default=10000,help="INT number of short reads")
parser.add_argument('--short_read_length',type=int,default=101,help="INT length of the short reads")
parser.add_argument('--long_read_count',type=int,default=4000,help="INT default number of long reads")
parser.add_argument('--no_errors',action='store_true')
parser.add_argument('--threads',type=int,default=1)
args = parser.parse_args()
if args.output:
args.output = args.output.rstrip('/')
fq_prof_pacbio_ccs95 = None
fq_prof_pacbio_subreads = None
fq_prof_illumina = None
if not args.no_errors:
fq_prof_pacbio_ccs95 = default_pacbio_ccs95()
fq_prof_pacbio_subreads = default_pacbio_subreads()
fq_prof_illumina = default_illumina()
ref = read_fasta_into_hash(args.reference_genome)
txn = Transcriptome()
txn.set_reference_genome_dictionary(ref)
with open(args.transcripts_genepred) as inf:
for line in inf:
if line[0]=='#': continue
txn.add_genepred_line(line.rstrip())
if args.isoform_expression:
sys.stderr.write("Reading expression from a TSV\n")
with open(args.isoform_expression) as inf:
line1 = inf.readline()
for line in inf:
f = line.rstrip().split("\t")
txn.add_expression(f[0],float(f[1]))
elif args.uniform_expression:
sys.stderr.write("Using uniform expression model\n")
elif args.cufflinks_isoform_expression:
sys.stderr.write("Using cufflinks expression\n")
with open(args.cufflinks_isoform_expression) as inf:
line1 = inf.readline()
for line in inf:
f = line.rstrip().split("\t")
txn.add_expression(f[0],float(f[9]))
sys.stderr.write("have transcriptome\n")
for n in txn.ref_hash.keys(): del txn.ref_hash[n]
rbe = SimulationBasics.RandomTranscriptomeEmitter(txn)
# Now we have the transcriptomes set
#Now our dataset is set up
if args.short_reads_only:
rbe.set_gaussian_fragmentation_default_hiseq()
for zi in range(0,args.short_read_count):
[name,seq] = rbe.emit_short_read(args.short_read_length)
if args.no_errors:
print "@SRSIM"+str(zi+1)
print seq
print "+"
print 'I'*len(seq)
else:
l1perm = fq_prof_illumina.create_fastq_and_permute_sequence(seq)
print "@SRSIM"+str(zi+1)
print l1perm['seq']
print "+"
print l1perm['qual']
return
if args.long_reads_only:
rbe.set_gaussian_fragmentation_default_pacbio()
for zi in range(0,args.long_read_count):
[name,seq] = rbe.emit_long_read()
if args.no_errors:
g = 'm150101_010101_11111_c111111111111111111_s1_p0/'+str(zi+1)+'/ccs'
print "@"+g
print seq
print "+"
print 'I'*len(seq)
else:
g = 'm150101_010101_11111_c111111111111111111_s1_p0/'+str(zi+1)+'/ccs'
seqperm = fq_prof_pacbio_ccs95.create_fastq_and_permute_sequence(seq)
print "@"+g
print seqperm['seq']
print "+"
print seqperm['qual']
return
if not os.path.exists(args.output):
os.makedirs(args.output)
rbe.set_gaussian_fragmentation_default_hiseq()
# Lets prepare to output now
sys.stderr.write("Sequencing short reads\n")
global left_handle
global right_handle
left_handle = gzip.open(args.output+"/SR_1.fq.gz",'wb')
right_handle = gzip.open(args.output+"/SR_2.fq.gz",'wb')
buffer_size = 10000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
z = 0
for i in range(0,args.short_read_count):
z = i+1
if z %1000==0: sys.stderr.write(str(z)+"\r")
buffer.append(z)
if len(buffer) >= buffer_size:
if args.threads <= 1:
v = process_short_read_buffer(buffer[:],rbe,args,fq_prof_illumina)
do_short(v)
else:
p.apply_async(process_short_read_buffer,args=(buffer[:],rbe,args,fq_prof_illumina),callback=do_short)
buffer = []
if len(buffer) > 0:
if args.threads <= 1:
v = process_short_read_buffer(buffer[:],rbe,args,fq_prof_illumina)
do_short(v)
else:
p.apply_async(process_short_read_buffer,args=(buffer[:],rbe,args,fq_prof_illumina),callback=do_short)
buffer = []
if args.threads > 1:
p.close()
p.join()
global greport
of = open(args.output+"/SR_report.txt",'w')
for name in greport:
of.write("\t".join([str(x) for x in greport[name]])+"\n")
of.close()
greport = {}
sys.stderr.write("\nFinished sequencing short reads\n")
left_handle.close()
right_handle.close()
# Now lets create the long read set
rbe.set_gaussian_fragmentation_default_pacbio()
sys.stderr.write("Sequencing ccs long reads\n")
global long_handle
long_handle = gzip.open(args.output+"/LR_ccs.fq.gz",'wb')
buffer_size = 1000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
z = 0
for i in range(0,args.long_read_count):
z = i+1
if z %100==0: sys.stderr.write(str(z)+"\r")
buffer.append(z)
if len(buffer) >= buffer_size:
if args.threads <= 1:
v = process_long_reads(buffer[:],rbe,args,fq_prof_pacbio_ccs95,'ccs')
do_long(v)
else:
p.apply_async(process_long_reads,args=(buffer[:],rbe,args,fq_prof_pacbio_ccs95,'ccs'),callback=do_long)
buffer = []
if len(buffer) > 0:
if args.threads <= 1:
v = process_long_reads(buffer[:],rbe,args,fq_prof_pacbio_ccs95,'ccs')
do_long(v)
else:
p.apply_async(process_long_reads,args=(buffer[:],rbe,args,fq_prof_pacbio_ccs95,'ccs'),callback=do_long)
buffer = []
if args.threads > 1:
p.close()
p.join()
long_handle.close()
of = open(args.output+"/LR_ccs_report.txt",'w')
for name in greport:
of.write("\t".join([str(x) for x in greport[name]])+"\n")
of.close()
greport = {}
sys.stderr.write("\nFinished sequencing ccs long reads\n")
sys.stderr.write("Sequencing long sub reads\n")
long_handle = gzip.open(args.output+"/LR_sub.fq.gz",'wb')
buffer_size = 1000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(z,z+args.long_read_count):
z = i+1
if z %100==0: sys.stderr.write(str(z)+"\r")
buffer.append(z)
if len(buffer) >= buffer_size:
if args.threads <= 1:
v = process_long_reads(buffer[:],rbe,args,fq_prof_pacbio_subreads,'sub')
do_long(v)
else:
p.apply_async(process_long_reads,args=(buffer[:],rbe,args,fq_prof_pacbio_subreads,'sub'),callback=do_long)
buffer = []
if len(buffer) > 0:
if args.threads <= 1:
v = process_long_reads(buffer[:],rbe,args,fq_prof_pacbio_subreads,'sub')
do_long(v)
else:
p.apply_async(process_long_reads,args=(buffer[:],rbe,args,fq_prof_pacbio_subreads,'sub'),callback=do_long)
buffer = []
if args.threads > 1:
p.close()
p.join()
long_handle.close()
of = open(args.output+"/LR_sub_report.txt",'w')
for name in greport:
of.write("\t".join([str(x) for x in greport[name]])+"\n")
of.close()
greport = {}
sys.stderr.write("\nFinished sequencing long sub reads\n")
combo = {}
with open(args.output+"/SR_report.txt") as inf:
for line in inf:
f = line.rstrip().split("\t")
[name,express,left] = f
if name not in combo:
combo[name] = {}
combo[name]['express'] = express
combo[name]['left'] = 0
combo[name]['left'] += int(left)
with open(args.output+"/LR_ccs_report.txt") as inf:
for line in inf:
f = line.rstrip().split("\t")
[name,express,left] = f
if name not in combo:
combo[name] = {}
combo[name]['express'] = express
combo[name]['left'] = 0
combo[name]['left'] += int(left)
with open(args.output+"/LR_sub_report.txt") as inf:
for line in inf:
f = line.rstrip().split("\t")
[name,express,left] = f
if name not in combo:
combo[name] = {}
combo[name]['express'] = express
combo[name]['left'] = 0
combo[name]['left'] += int(left)
of = open(args.output+"/LR_SR_combo_report.txt",'w')
for name in sorted(combo):
of.write(name+"\t"+combo[name]['express']+"\t"+str(combo[name]['left'])+"\n")
of.close()
def main():
parser = argparse.ArgumentParser(description="Create a simulated RNA-seq dataset")
group0 = parser.add_mutually_exclusive_group(required=True)
group0.add_argument('--load_biallelic_transcriptome',help="SERIALIZED BIALLELIC TRANSCRIOTOME EMITTER FILE to load up and use instead of all other file inputs")
group0.add_argument('--inputs',nargs=3,help="<reference_genome> <phased_VCF> <transcripts_genepred>")
#parser.add_argument('reference_genome',help="The reference genome.")
#parser.add_argument('phased_VCF',help="A phased VCF file. If you are simulating the genomes that step can make on of these for you.")
#parser.add_argument('transcripts_genepred',help="A genepred file describing the transcripts. Each transcript name must be unique.")
group = parser.add_mutually_exclusive_group()
group.add_argument('--uniform_expression',action='store_true',help="Uniform distribution of transcript expression")
group.add_argument('--isoform_expression',help="The transcript expression in TSV format <Transcript name> tab <Expression>")
group.add_argument('--cufflinks_isoform_expression',help="The expression of the isoforms or - for a uniform distribution of transcript expression")
group2 = parser.add_mutually_exclusive_group()
group2.add_argument('--ASE_identical',type=float,help="The ASE for the transcriptome, every isoform will have the same allele preference.")
group2.add_argument('--ASE_isoform_random',action='store_true',help="The ASE will be random for every isoform.")
group2.add_argument('--ASE_locus_random',action='store_true',help="The ASE will be randomly assigned for each locus")
parser.add_argument('--short_read_count',type=int,default=10000,help="INT number of short reads")
parser.add_argument('--short_read_length',type=int,default=101,help="INT length of the short reads")
parser.add_argument('--long_read_ccs_count',type=int,default=4000,help="INT default number of long reads")
parser.add_argument('--long_read_subread_count',type=int,default=4000,help="INT default number of long reads")
parser.add_argument('--no_errors',action='store_true',help="Do not simulate errors in reads")
parser.add_argument('--threads',type=int,default=cpu_count(),help="Number of threads defaults to cpu_count()")
parser.add_argument('--locus_by_gene_name',action='store_true',help="Faster than the complete calculation for overlapping loci.")
parser.add_argument('--seed',type=int,help="seed to make transcriptome and rho creation deterministic. Reads are still random, its just the transcriptome and rho that become determinisitic.")
group3 = parser.add_mutually_exclusive_group(required=True)
group3.add_argument('--output',help="Directory name for output")
group3.add_argument('--save_biallelic_transcriptome',help="FILENAME output the biallelic transcriptome used to this file and then exit")
parser.add_argument('--starting_read_multiplier',type=int,default=0,help="Used if outputting different reads from object, and you want them number differently give each different set values 0, 1, 2, etc...")
args = parser.parse_args()
fq_prof_illumina = None
fq_prof_pacbio_ccs95 = None
fq_prof_pacbio_subreads = None
if not args.no_errors:
fq_prof_illumina = default_illumina()
fq_prof_pacbio_ccs95 = default_pacbio_ccs95()
fq_prof_pacbio_subreads = default_pacbio_subreads()
rbe = None
if not args.load_biallelic_transcriptome:
# we need to establish the emitter based on some known data
rbe = load_from_inputs(args)
else:
rbe = SimulationBasics.RandomBiallelicTranscriptomeEmitter()
inf = open(args.load_biallelic_transcriptome)
sline = inf.readline().rstrip()
inf.close()
rbe.read_serialized(sline)
if args.save_biallelic_transcriptome:
ofser = open(args.save_biallelic_transcriptome,'w')
ofser.write(rbe.get_serialized())
ofser.close()
return #exiting here
# Lets prepare to output now
args.output = args.output.rstrip('/')
if not os.path.exists(args.output):
os.makedirs(args.output)
ofser = open(args.output+"/RandomBiallelicTranscriptomeEmitter.serialized",'w')
ofser.write(rbe.get_serialized())
ofser.close()
rbe.set_gaussian_fragmentation_default_hiseq()
#rbe_ser = rbe.get_serialized()
sys.stderr.write("Sequencing short reads\n")
global shand1
shand1 = gzip.open(args.output+"/SR_1.fq.gz",'wb')
global shand2
shand2 = gzip.open(args.output+"/SR_2.fq.gz",'wb')
z = 0
buffer_full_size = 5000
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(args.short_read_count*args.starting_read_multiplier,args.short_read_count*(args.starting_read_multiplier+1)):
z = i+1
buffer.append(z)
if buffer_full_size <= len(buffer):
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_short_read_buffer,args=(rbe,vals,args),callback=write_short_reads)
else:
oval = process_short_read_buffer(rbe,vals,args)
write_short_reads(oval)
if len(buffer) > 0:
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_short_read_buffer,args=(rbe,vals,args),callback=write_short_reads)
else:
oval = process_short_read_buffer(rbe,vals,args)
write_short_reads(oval)
if args.threads > 1:
p.close()
p.join()
sys.stderr.write("\nFinished sequencing short reads\n")
shand1.close()
shand2.close()
global emissions_reports
for i in range(0,len(emissions_reports)): emissions_reports[i]= emissions_reports[i].get()
sr_report = combine_reports(emissions_reports)
rbe.emissions_report = {} # initialize so we don't accidentally overwrite
# Now lets print out some of the emission details
of = open(args.output+"/SR_report.txt",'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in sr_report:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(sr_report[name][0])+"\t"+str(sr_report[name][1])+"\n")
else:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(0)+"\t"+str(0)+"\n")
of.close()
rbe.emissions_report = {}
emissions_reports = []
# Now lets create the long read set
rbe.set_gaussian_fragmentation_default_pacbio()
#rbe_ser = rbe.get_serialized()
sys.stderr.write("Sequencing long ccs reads\n")
shand1 = gzip.open(args.output+"/LR_ccs95.fq.gz",'wb')
buffer_full_size = 500
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(args.starting_read_multiplier*args.long_read_ccs_count,(args.starting_read_multiplier+1)*args.long_read_ccs_count):
z = i+1
buffer.append(z)
if buffer_full_size <= len(buffer):
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_ccs_read_buffer,args=(rbe,vals,args),callback=write_long_reads)
else:
oval = process_long_ccs_read_buffer(rbe,vals,args)
write_long_reads(oval)
if len(buffer) > 0:
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_ccs_read_buffer,args=(rbe,vals,args),callback=write_long_reads)
else:
oval = process_long_ccs_read_buffer(rbe,vals,args)
write_long_reads(oval)
if args.threads > 1:
p.close()
p.join()
sys.stderr.write("\nFinished sequencing long reads\n")
shand1.close()
for i in range(0,len(emissions_reports)): emissions_reports[i]= emissions_reports[i].get()
lr_ccs_report = combine_reports(emissions_reports)
rbe.emissions_report = {} # initialize so we don't accidentally overwrite
# Now lets print out some of the emission details
of = open(args.output+"/LR_ccs95_report.txt",'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in lr_ccs_report:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(lr_ccs_report[name][0])+"\t"+str(lr_ccs_report[name][1])+"\n")
else:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(0)+"\t"+str(0)+"\n")
of.close()
rbe.emissions_report = {}
emissions_reports = []
# Now lets create the long subread read set
rbe.set_gaussian_fragmentation_default_pacbio()
#rbe_ser = rbe.get_serialized()
sys.stderr.write("Sequencing long subreads\n")
shand1 = gzip.open(args.output+"/LR_subreads.fq.gz",'wb')
buffer_full_size = 500
buffer = []
if args.threads > 1:
p = Pool(processes=args.threads)
for i in range(args.long_read_subread_count*args.starting_read_multiplier,(args.starting_read_multiplier+1)*args.long_read_subread_count):
z = i+1
buffer.append(z)
if buffer_full_size <= len(buffer):
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_sub_read_buffer,args=(rbe,vals,args),callback=write_long_reads)
else:
oval = process_long_sub_read_buffer(rbe,vals,args)
write_long_reads(oval)
if len(buffer) > 0:
vals = buffer[:]
buffer = []
if args.threads > 1:
p.apply_async(process_long_sub_read_buffer,args=(rbe,vals,args),callback=write_long_reads)
else:
oval = process_long_sub_read_buffer(rbe,vals,args)
write_long_reads(oval)
if args.threads > 1:
p.close()
p.join()
sys.stderr.write("\nFinished sequencing long reads\n")
shand1.close()
for i in range(0,len(emissions_reports)): emissions_reports[i]= emissions_reports[i].get()
lr_sub_report = combine_reports(emissions_reports)
rbe.emissions_report = {} # initialize so we don't accidentally overwrite
# Now lets print out some of the emission details
of = open(args.output+"/LR_subreads_report.txt",'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in lr_sub_report:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(lr_sub_report[name][0])+"\t"+str(lr_sub_report[name][1])+"\n")
else:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(0)+"\t"+str(0)+"\n")
of.close()
combo_report = combine_reports([sr_report,lr_ccs_report,lr_sub_report])
of = open(args.output+"/LR_SR_combo_report.txt",'w')
for name in sorted(rbe.name2locus.keys()):
express = 1
if rbe.transcriptome1.expression:
express = rbe.transcriptome1.expression.get_expression(name)
if name in combo_report:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(combo_report[name][0])+"\t"+str(combo_report[name][1])+"\n")
else:
of.write(name +"\t"+rbe.gene_names[name]+"\t"+str(rbe.name2locus[name])+"\t"+str(express)+"\t"+str(rbe.transcriptome1_rho[name])+"\t"+str(0)+"\t"+str(0)+"\n")
of.close()