def main(argv=None):
settings = process_command_line(argv)
# Read the transcripts if given
if settings.transcripts:
trans_dict = RILseq.read_transcripts(settings.transcripts)
else:
trans_dict = None
# Get the ends of the reads from the bam files
# sys.stderr.write('%s\n'%str(settings.bamfiles))
if settings.all_reads:
try:
outall = open(settings.all_reads, 'w')
except IOError:
outall = None
elif settings.add_all_reads:
outall = sys.stdout
else:
outall = None
for bf in RILseq.flat_list(settings.bamfiles):
bfin = pysam.Samfile(bf)
outhead = bf.rsplit('.', 1)[0]
libname = outhead.rsplit('/',1)[-1]
fsq1name = "%s/%s_ends_1.fastq"%(settings.dirout, libname)
fsq2name = "%s/%s_ends_2.fastq"%(settings.dirout, libname)
if settings.skip_mapping:
fsq1 = open(os.devnull, 'w')
fsq2 = fsq1
else:
fsq1 = open(fsq1name, 'w')
fsq2 = open(fsq2name, 'w')
single_mapped = RILseq.get_unmapped_reads(
bfin, fsq1, fsq2, settings.length, settings.maxG,
rev=settings.reverse_complement, all_reads=True,
dust_thr=settings.dust_thr)
reads_in = []
# Map the fastq files to the genome
for fqname in (fsq1name, fsq2name):
bamheadname = fqname.rsplit('.',1)[0].rsplit('/',1)[-1]
if settings.skip_mapping:
bamname = "%s/%s.bam"%(settings.dirout, bamheadname)
else:
bamname = RILseq.run_bwa(
settings.bwa_exec, fqname, None,
settings.dirout, bamheadname, settings.max_mismatches,
settings.genome_fasta, settings.params_aln,
'', settings.samse_params,
settings.samtools_cmd, processors=settings.processors)
bamin = pysam.Samfile(bamname)
reads_in.append(RILseq.read_bam_file(
bamin, bamin.references, settings.allowed_mismatches))
RILseq.write_reads_table(
sys.stdout, reads_in[0], reads_in[1], bfin.references,
settings.distance, not settings.keep_circular,
trans_dict, write_single=outall, single_mapped=single_mapped,
max_NM=settings.allowed_mismatches)
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)
# Read the transcripts if given
if settings.transcripts:
trans_dict = RILseq.read_transcripts(settings.transcripts)
else:
trans_dict = None
# Get the ends of the reads from the bam files
# sys.stderr.write('%s\n'%str(settings.bamfiles))
if settings.all_reads:
try:
outall = open(settings.all_reads, 'w')
except IOError:
outall = None
elif settings.add_all_reads:
outall = sys.stdout
else:
outall = None
for bf in RILseq.flat_list(settings.bamfiles):
bfin = pysam.Samfile(bf)
outhead = bf.rsplit('.', 1)[0]
libname = outhead.rsplit('/', 1)[-1]
fsq1name = "%s/%s_ends_1.fastq" % (settings.dirout, libname)
fsq2name = "%s/%s_ends_2.fastq" % (settings.dirout, libname)
if settings.skip_mapping:
fsq1 = open(os.devnull, 'w')
fsq2 = fsq1
else:
fsq1 = open(fsq1name, 'w')
fsq2 = open(fsq2name, 'w')
single_mapped = RILseq.get_unmapped_reads(
bfin,
fsq1,
fsq2,
settings.length,
settings.maxG,
rev=settings.reverse_complement,
all_reads=True,
dust_thr=settings.dust_thr)
reads_in = []
# Map the fastq files to the genome
for fqname in (fsq1name, fsq2name):
bamheadname = fqname.rsplit('.', 1)[0].rsplit('/', 1)[-1]
if settings.skip_mapping:
bamname = "%s/%s.bam" % (settings.dirout, bamheadname)
else:
bamname = RILseq.run_bwa(settings.bwa_exec,
fqname,
None,
settings.dirout,
bamheadname,
settings.max_mismatches,
settings.genome_fasta,
settings.params_aln,
'',
settings.samse_params,
settings.samtools_cmd,
processors=settings.processors)
bamin = pysam.Samfile(bamname)
reads_in.append(
RILseq.read_bam_file(bamin, bamin.references,
settings.allowed_mismatches))
RILseq.write_reads_table(sys.stdout,
reads_in[0],
reads_in[1],
bfin.references,
settings.distance,
not settings.keep_circular,
trans_dict,
write_single=outall,
single_mapped=single_mapped,
max_NM=settings.allowed_mismatches)
return 0 # success
