def quantitate_expression_parallel(samples, run_parallel):
"""
quantitate expression, all programs run here should be multithreaded to
take advantage of the threaded run_parallel environment
"""
data = samples[0][0]
samples = run_parallel("generate_transcript_counts", samples)
samples = run_parallel("run_sailfish", samples)
samples = sailfish.combine_sailfish(samples)
if "cufflinks" in dd.get_expression_caller(data):
samples = run_parallel("run_cufflinks", samples)
#samples = run_parallel("run_stringtie_expression", samples)
return samples
def quantitate_expression_parallel(samples, run_parallel):
"""
quantitate expression, all programs run here should be multithreaded to
take advantage of the threaded run_parallel environment
"""
samples = run_parallel("generate_transcript_counts", samples)
samples = run_parallel("run_cufflinks", samples)
data = samples[0][0]
if "sailfish" in dd.get_expression_caller(data):
samples = run_parallel("run_sailfish", samples)
samples = sailfish.combine_sailfish(samples)
#samples = run_parallel("run_stringtie_expression", samples)
return samples
def fast_rnaseq(samples, run_parallel):
samples = run_parallel("run_salmon_index", [samples])
samples = run_parallel("run_salmon_reads", samples)
samples = sailfish.combine_sailfish(samples)
return samples
def fast_rnaseq(samples, run_parallel):
# samples = run_parallel("run_rapmap_pseudoalign", samples)
samples = run_parallel("run_salmon_reads", samples)
samples = sailfish.combine_sailfish(samples)
# samples = run_parallel("run_salmon_bam", samples)
return samples
def fast_rnaseq(samples, run_parallel):
# samples = run_parallel("run_rapmap_pseudoalign", samples)
samples = run_parallel("run_salmon_reads", samples)
samples = sailfish.combine_sailfish(samples)
# samples = run_parallel("run_salmon_bam", samples)
return samples
def fast_rnaseq(samples, run_parallel):
samples = run_parallel("run_salmon_reads", samples)
samples = sailfish.combine_sailfish(samples)
return samples
