def run_salmon_bam(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) bam_file = dd.get_transcriptome_bam(data) fasta_file = dd.get_ref_file(data) out_file = salmon_quant_bam(bam_file, salmon_dir, gtf_file, fasta_file, data) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) return [[data]]
def run_salmon_bam(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) bam_file = dd.get_transcriptome_bam(data) fasta_file = dd.get_ref_file(data) out_file = salmon_quant_bam(bam_file, salmon_dir, gtf_file, fasta_file, data) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) data = dd.set_salmon_fraglen_file(data, _get_fraglen_file(salmon_dir)) return [[data]]
def run_salmon_bam(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) bam_file = dd.get_transcriptome_bam(data) out_file = salmon_quant_bam(bam_file, salmon_dir, gtf_file, data) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) data = dd.set_salmon_fraglen_file(data, _get_fraglen_file(salmon_dir)) data = dd.update_summary_qc(data, "salmon", base=dd.get_salmon_fraglen_file(data)) return [[data]]
def run_salmon_bam(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) bam_file = dd.get_transcriptome_bam(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 out_file = salmon_quant_bam(bam_file, salmon_dir, gtf_file, fasta_file, data) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) return [[data]]
def run_salmon_reads(data): data = utils.to_single_data(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 fasta_file = dd.get_ref_file(data) out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, fasta_file, data) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) return [[data]]
def run_salmon_reads(data): data = utils.to_single_data(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_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) return [[data]]
def run_salmon_reads(data): data = utils.to_single_data(data) files = dd.get_input_sequence_files(data) if bam.is_bam(files[0]): files = fastq.convert_bam_to_fastq(files[0], data["dirs"]["work"], data, data["dirs"], data["config"]) 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) if len(files) == 2: fq1, fq2 = files else: fq1, fq2 = files[0], None fasta_file = dd.get_ref_file(data) out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, fasta_file, data) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) data = dd.set_salmon_fraglen_file(data, _get_fraglen_file(salmon_dir)) return [[data]]
def run_salmon_reads(data): data = utils.to_single_data(data) files = dd.get_input_sequence_files(data) if bam.is_bam(files[0]): files = fastq.convert_bam_to_fastq(files[0], data["dirs"]["work"], data, data["dirs"], data["config"]) 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) if len(files) == 2: fq1, fq2 = files else: fq1, fq2 = files[0], None fasta_file = dd.get_ref_file(data) out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, fasta_file, data) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) return [[data]]
def run_salmon_decoy(data): data = utils.to_single_data(data) files = dd.get_input_sequence_files(data) if bam.is_bam(files[0]): files = fastq.convert_bam_to_fastq(files[0], data["dirs"]["work"], data, data["dirs"], data["config"]) 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) if len(files) == 2: fq1, fq2 = files else: fq1, fq2 = files[0], None index = salmon_decoy_index(gtf_file, data, os.path.dirname(salmon_dir)) out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, data, index) data = dd.set_salmon(data, out_file) data = dd.set_salmon_dir(data, salmon_dir) data = dd.set_salmon_fraglen_file(data, _get_fraglen_file(salmon_dir)) data = dd.update_summary_qc(data, "salmon", base=dd.get_salmon_fraglen_file(data)) return [[data]]