def main(argv=None):
settings = process_command_line(argv)
try:
pos_feat_list, all_features = RILseq.read_gtf(
open(settings.genes_gff), settings.feature, settings.identifier)
except IOError:
return 1
lib_order = []
all_counts = {}
if settings.singles:
settings.only_first = True
settings.only_second = False
for r1_name in RILseq.flat_list(settings.reads_files):
sys.stderr.write('%s\n'%str(r1_name))
lib_order.append(r1_name)
all_counts[r1_name] = count_features(
pos_feat_list, open(r1_name), settings.overlap, length=25,
ignore_first=settings.only_second,
ignore_second=settings.only_first, count_singles=settings.singles)
outt = csv.writer(sys.stdout, delimiter='\t')
if not settings.quiet:
outt.writerow(['Gene name'] + lib_order)
for g in sorted(list(all_features)):
if settings.quiet and g.startswith('~'):
continue
row_out = [g]
for libn in lib_order:
row_out.append(all_counts[libn][g])
outt.writerow(row_out)
# application code here, like:
# run(settings, args)
return 0 # success
def main(argv=None):
settings = process_command_line(argv)
if not os.path.exists(settings.dirout):
os.makedirs(settings.dirout)
if settings.genes_gff:
try:
pos_feat_list, all_features = RILseq.read_gtf(
open(settings.genes_gff), settings.feature, settings.identifier)
except IOError:
settings.genes_gff = None
gcounts = {}
lib_order = []
fastq_1_list = list(RILseq.flat_list(settings.fastq_1))
fastq_2_list = list(RILseq.flat_list(settings.fastq_2))
for i, r1_name in enumerate(RILseq.flat_list(settings.fastq_1)):
try:
r2_name = fastq_2_list[i]
except IndexError:
r2_name = None
outhead = r1_name.rsplit('.', 1)[0]
libname = outhead.rsplit('/',1)[-1]
outhead = '%s_bwa'%libname
bamname = RILseq.run_bwa(
settings.bwa_exec, r1_name, r2_name,
settings.dirout, outhead, settings.allowed_mismatches,
settings.genome_fasta, settings.params_aln, settings.sampe_params,
settings.samse_params, settings.samtools_cmd)
samfile = pysam.Samfile(bamname)
if settings.genes_gff:
lib_order.append(libname)
gcounts[libname] = RILseq.count_features(
pos_feat_list, samfile, settings.overlap,
rev=settings.reverse_complement)
if settings.create_wig:
outwigs = [open("%s/%s_coverage.wig"%(settings.dirout, fastq.split("_cutadapt")[0]), 'w')
for fastq in fastq_1_list]
coverage = RILseq.generate_wig(
samfile, rev=settings.reverse_complement, first_pos=False)
RILseq.print_wiggle(
coverage, "%s_single_fragments_coverage"%libname,
"%s single fragments coverage"%libname, outwigs[i])
# Print the table of counts
if settings.genes_gff:
outtables = [open("%s/%s_counts.txt"%(settings.dirout, fastq.split("_cutadapt")[0]), 'w')
for fastq in fastq_1_list]
for i, r1_name in enumerate(fastq_1_list):
outt = csv.writer(outtables[i], delimiter='\t')
outt.writerow(['Gene name'] + lib_order)
for g in sorted(list(all_features)):
row_out = [g]
for libn in lib_order:
row_out.append(gcounts[libn][g])
outt.writerow(row_out)
return 0 # success
def main(argv=None):
settings = process_command_line(argv)
if not os.path.exists(settings.dirout):
os.makedirs(settings.dirout)
outwig = open("%s/%s_coverage.wig"%(settings.dirout, settings.outhead), 'w')
if settings.genes_gff:
try:
pos_feat_list, all_features = RILseq.read_gtf(
open(settings.genes_gff), settings.feature, settings.identifier)
except IOError:
settings.genes_gff = None
gcounts = {}
lib_order = []
fastq_2_list = list(RILseq.flat_list(settings.fastq_2))
for i, r1_name in enumerate(RILseq.flat_list(settings.fastq_1)):
try:
r2_name = fastq_2_list[i]
except IndexError:
r2_name = None
outhead = r1_name.rsplit('.', 1)[0]
libname = outhead.rsplit('/',1)[-1]
outhead = '%s_bwa'%libname
bamname = RILseq.run_bwa(
settings.bwa_exec, r1_name, r2_name,
settings.dirout, outhead, settings.allowed_mismatches,
settings.genome_fasta, settings.params_aln, settings.sampe_params,
settings.samse_params, settings.samtools_cmd,
processors=settings.processors)
samfile = pysam.Samfile(bamname)
if settings.genes_gff:
lib_order.append(libname)
gcounts[libname] = RILseq.count_features(
pos_feat_list, samfile, settings.overlap,
rev=settings.reverse_complement)
coverage = RILseq.generate_wig(
samfile, rev=settings.reverse_complement, first_pos=False)
RILseq.print_wiggle(
coverage, "%s_single_fragments_coverage"%libname,
"%s single fragments coverage"%libname, outwig)
# Print the table of counts
if settings.genes_gff:
outtable = open(
"%s/%s_counts.txt"%(settings.dirout, settings.outhead), 'w')
outt = csv.writer(outtable, delimiter='\t')
outt.writerow(['Gene name'] + lib_order)
for g in sorted(list(all_features)):
row_out = [g]
for libn in lib_order:
row_out.append(gcounts[libn][g])
outt.writerow(row_out)
return 0 # success
def main(argv=None):
settings = process_command_line(argv)
try:
pos_feat_list, all_features = RILseq.read_gtf(open(settings.genes_gff),
settings.feature,
settings.identifier)
except IOError:
return 1
lib_order = []
all_counts = {}
if settings.singles:
settings.only_first = True
settings.only_second = False
for r1_name in RILseq.flat_list(settings.reads_files):
sys.stderr.write('%s\n' % str(r1_name))
lib_order.append(r1_name)
all_counts[r1_name] = count_features(pos_feat_list,
open(r1_name),
settings.overlap,
length=25,
ignore_first=settings.only_second,
ignore_second=settings.only_first,
count_singles=settings.singles)
outt = csv.writer(sys.stdout, delimiter='\t')
if not settings.quiet:
outt.writerow(['Gene name'] + lib_order)
for g in sorted(list(all_features)):
if settings.quiet and g.startswith('~'):
continue
row_out = [g]
for libn in lib_order:
row_out.append(all_counts[libn][g])
outt.writerow(row_out)
# application code here, like:
# run(settings, args)
return 0 # success
