def generate_transcript_counts(data): """Generate counts per transcript and per exon from an alignment""" data["count_file"] = featureCounts.count(data) if dd.get_transcriptome_align(data): # to create a disambiguated transcriptome file realign with bowtie2 if dd.get_disambiguate(data): logger.info("Aligning to the transcriptome with bowtie2 using the " "disambiguated reads.") bam_path = data["work_bam"] fastq_paths = alignprep._bgzip_from_bam( bam_path, data["dirs"], data, is_retry=False, output_infix='-transcriptome') if len(fastq_paths) == 2: file1, file2 = fastq_paths else: file1, file2 = fastq_paths[0], None ref_file = dd.get_ref_file(data) data = bowtie2.align_transcriptome(file1, file2, ref_file, data) else: file1, file2 = dd.get_input_sequence_files(data) if not dd.get_transcriptome_bam(data): ref_file = dd.get_ref_file(data) logger.info( "Transcriptome alignment was flagged to run, but the " "transcriptome BAM file was not found. Aligning to the " "transcriptome with bowtie2.") data = bowtie2.align_transcriptome(file1, file2, ref_file, data) data = spikein.counts_spikein(data) return [[data]]
def generate_transcript_counts(data): """Generate counts per transcript and per exon from an alignment""" data["count_file"] = featureCounts.count(data) if dd.get_fusion_mode(data, False): oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) if dd.get_transcriptome_align(data): # to create a disambiguated transcriptome file realign with bowtie2 if dd.get_disambiguate(data): logger.info("Aligning to the transcriptome with bowtie2 using the " "disambiguated reads.") bam_path = data["work_bam"] fastq_paths = alignprep._bgzip_from_bam(bam_path, data["dirs"], data["config"], is_retry=False, output_infix='-transcriptome') if len(fastq_paths) == 2: file1, file2 = fastq_paths else: file1, file2 = fastq_paths[0], None ref_file = dd.get_ref_file(data) data = bowtie2.align_transcriptome(file1, file2, ref_file, data) else: file1, file2 = dd.get_input_sequence_files(data) if not dd.get_transcriptome_bam(data): ref_file = dd.get_ref_file(data) logger.info("Transcriptome alignment was flagged to run, but the " "transcriptome BAM file was not found. Aligning to the " "transcriptome with bowtie2.") data = bowtie2.align_transcriptome(file1, file2, ref_file, data) return [[data]]
def generate_transcript_counts(data): """Generate counts per transcript and per exon from an alignment""" data["count_file"] = featureCounts.count(data) if dd.get_fusion_mode(data, False): oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) if dd.get_transcriptome_align(data) and not dd.get_transcriptome_bam(data): file1, file2 = None, None if dd.get_disambiguate(data): bam_path = data["work_bam"] fastq_paths = alignprep._bgzip_from_bam( bam_path, data["dirs"], data["config"], is_retry=False, output_infix='-transcriptome') if len(fastq_paths) == 2: file1, file2 = fastq_paths else: file1, file2 = fastq_paths[0], None else: file1, file2 = dd.get_input_sequence_files(data) ref_file = dd.get_ref_file(data) logger.info("Transcriptome alignment was flagged to run, but the " "transcriptome BAM file was not found. Aligning to the " "transcriptome with bowtie2.") data = bowtie2.align_transcriptome(file1, file2, ref_file, data) return [[data]]
def generate_transcript_counts(data): """Generate counts per transcript and per exon from an alignment""" data["count_file"] = featureCounts.count(data) if dd.get_fusion_mode(data, False): oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) # if RSEM set to run, but the aligner didn't create the transcriptome BAM # file, make one with bwa if dd.get_rsem(data) and not dd.get_transcriptome_bam(data): file1, file2 = dd.get_input_sequence_files(data) ref_file = dd.get_ref_file(data) logger.info("RSEM was flagged to run, but the transcriptome BAM file " "was not found. Aligning to the transcriptome with bowtie2.") data = bowtie2.align_transcriptome(file1, file2, ref_file, data) return [[data]]
def generate_transcript_counts(data): """Generate counts per transcript and per exon from an alignment""" data["count_file"] = featureCounts.count(data) if dd.get_fusion_mode(data, False): oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) # if RSEM set to run, but the aligner didn't create the transcriptome BAM # file, make one with bwa if dd.get_rsem(data) and not dd.get_transcriptome_bam(data): file1, file2 = dd.get_input_sequence_files(data) ref_file = dd.get_ref_file(data) logger.info( "RSEM was flagged to run, but the transcriptome BAM file " "was not found. Aligning to the transcriptome with bowtie2.") data = bowtie2.align_transcriptome(file1, file2, ref_file, data) return [[data]]
def generate_transcript_counts(data): """Generate counts per transcript and per exon from an alignment""" data["count_file"] = featureCounts.count(data) if dd.get_fusion_mode(data, False): oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) # if RSEM set to run, but the aligner didn't create the transcriptome BAM # file, make one with bwa if dd.get_disambiguate(data): logger.info("RSEM is not supported yet for disambiguation protocols. " "See https://github.com/chapmanb/bcbio-nextgen/issues/859") return [[data]] if dd.get_rsem(data) and not dd.get_transcriptome_bam(data): file1, file2 = dd.get_input_sequence_files(data) ref_file = dd.get_ref_file(data) logger.info("RSEM was flagged to run, but the transcriptome BAM file " "was not found. Aligning to the transcriptome with bowtie2.") data = bowtie2.align_transcriptome(file1, file2, ref_file, data) return [[data]]