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
"""
assembler = dd.get_in_samples(samples, dd.get_transcript_assembler)
data = samples[0][0]
if assembler:
if "cufflinks" in assembler:
samples = run_parallel("cufflinks_assemble", samples)
if "stringtie" in assembler:
samples = run_parallel("run_stringtie_expression", samples)
if "stringtie" in assembler and stringtie.supports_merge(data):
samples = run_parallel("stringtie_merge", [samples])
else:
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
"""
assembler = dd.get_in_samples(samples, dd.get_transcript_assembler)
data = samples[0][0]
if assembler:
if "cufflinks" in assembler:
samples = run_parallel("cufflinks_assemble", samples)
if "stringtie" in assembler:
samples = run_parallel("run_stringtie_expression", samples)
if "stringtie" in assembler and stringtie.supports_merge(data):
samples = run_parallel("stringtie_merge", [samples])
else:
samples = run_parallel("cufflinks_merge", [samples])
return samples
