def run_salmon_reads(data): samplename = dd.get_sample_name(data) work_dir = dd.get_work_dir(data) salmon_dir = os.path.join(work_dir, "salmon", samplename) gtf_file = dd.get_gtf_file(data) files = dd.get_input_sequence_files(data) if len(files) == 2: fq1, fq2 = files else: fq1, fq2 = files[0], None assert file_exists(gtf_file), "%s was not found, exiting." % gtf_file fasta_file = dd.get_ref_file(data) assert file_exists(fasta_file), "%s was not found, exiting." % fasta_file out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, fasta_file, data) data = dd.set_sailfish(data, out_file) data = dd.set_sailfish_dir(data, salmon_dir) return [[data]]
def run_sailfish(data): samplename = dd.get_sample_name(data) files = dd.get_input_sequence_files(data) work_dir = dd.get_work_dir(data) if len(files) == 2: fq1, fq2 = files else: fq1, fq2 = files[0], None if not fastq.is_fastq(fq1): return [[data]] sailfish_dir = os.path.join(work_dir, "sailfish", samplename) gtf_file = dd.get_gtf_file(data) assert file_exists(gtf_file), "%s was not found, exiting." % gtf_file fasta_file = dd.get_ref_file(data) assert file_exists(fasta_file), "%s was not found, exiting." % fasta_file stranded = dd.get_strandedness(data).lower() out_file = sailfish(fq1, fq2, sailfish_dir, gtf_file, fasta_file, stranded, data) data = dd.set_sailfish(data, out_file) data = dd.set_sailfish_dir(data, sailfish_dir) return [[data]]