def align(fastq_file, pair_file, ref_file, names, align_dir, data):
paired = True if pair_file else False
hisat2 = config_utils.get_program("hisat2", data)
num_cores = dd.get_num_cores(data)
quality_flag = _get_quality_flag(data)
stranded_flag = _get_stranded_flag(data, paired)
rg_flags = _get_rg_flags(names)
out_file = os.path.join(align_dir, dd.get_lane(data)) + ".bam"
if file_exists(out_file):
data = dd.set_work_bam(data, out_file)
return data
cmd = (
"{hisat2} -x {ref_file} -p {num_cores} {quality_flag} {stranded_flag} "
"{rg_flags} ")
if paired:
cmd += "-1 {fastq_file} -2 {pair_file} "
else:
cmd += "-U {fastq_file} "
if dd.get_analysis(data).lower() == "smallrna-seq":
cmd += "-k 1000 "
# if assembling transcripts, set flags that cufflinks can use
if dd.get_assemble_transcripts(data):
cmd += "--dta-cufflinks "
if dd.get_analysis(data).lower() == "rna-seq":
gtf_file = dd.get_gtf_file(data)
splicesites = os.path.join(os.path.dirname(gtf_file),
"ref-transcripts-splicesites.txt")
cmd += "--known-splicesite-infile {splicesites} "
message = "Aligning %s and %s with hisat2." % (fastq_file, pair_file)
with file_transaction(out_file) as tx_out_file:
cmd += " | " + postalign.sam_to_sortbam_cl(data, tx_out_file)
do.run(cmd.format(**locals()), message)
data = dd.set_work_bam(data, out_file)
return data
def align(fastq_file, pair_file, ref_file, names, align_dir, data):
paired = True if pair_file else False
hisat2 = config_utils.get_program("hisat2", data)
num_cores = dd.get_num_cores(data)
quality_flag = _get_quality_flag(data)
stranded_flag = _get_stranded_flag(data, paired)
rg_flags = _get_rg_flags(names)
out_file = os.path.join(align_dir, dd.get_lane(data)) + ".bam"
if file_exists(out_file):
data = dd.set_work_bam(data, out_file)
return data
cmd = ("{hisat2} -x {ref_file} -p {num_cores} {quality_flag} {stranded_flag} "
"{rg_flags} ")
if paired:
cmd += "-1 {fastq_file} -2 {pair_file} "
else:
cmd += "-U {fastq_file} "
if dd.get_analysis(data).lower() == "smallrna-seq":
cmd += "-k 1000 "
# if assembling transcripts, set flags that cufflinks can use
if dd.get_assemble_transcripts(data):
cmd += "--dta-cufflinks "
if dd.get_analysis(data) == "rna-seq":
splicesites = os.path.join(os.path.dirname(gtf_file),
"ref-transcripts-splicesites.txt")
cmd += "--known-splicesite-infile {splicesites} "
message = "Aligning %s and %s with hisat2." %(fastq_file, pair_file)
with file_transaction(out_file) as tx_out_file:
cmd += " | " + postalign.sam_to_sortbam_cl(data, tx_out_file)
do.run(cmd.format(**locals()), message)
data = dd.set_work_bam(data, out_file)
return data
def assemble_transcripts(run_parallel, samples):
"""
assembly strategy rationale implemented as suggested in
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
run Cufflinks in without a reference GTF for each individual sample
merge the assemblies with Cuffmerge using a reference GTF
"""
if dd.get_assemble_transcripts(samples[0][0]):
samples = run_parallel("cufflinks_assemble", samples)
samples = run_parallel("cufflinks_merge", [samples])
return samples
def assemble_transcripts(run_parallel, samples):
"""
assembly strategy rationale implemented as suggested in
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
run Cufflinks in without a reference GTF for each individual sample
merge the assemblies with Cuffmerge using a reference GTF
"""
if dd.get_assemble_transcripts(samples[0][0]):
samples = run_parallel("cufflinks_assemble", samples)
samples = run_parallel("cufflinks_merge", [samples])
return samples
