omicverse.alignment.featureCount¶
- omicverse.alignment.featureCount(bam_items, gtf, output_dir='counts', threads=8, jobs=None, max_workers=None, simple=True, merge_matrix=True, quiet=True, gene_mapping=False, gene_map=None, gene_name_field='gene_name', overwrite=False, featurecounts_path=None, auto_install=True, strict=False, auto_fix=True)[source]¶
Run featureCounts on BAM files.
- Parameters:
bam_items (
Union[Tuple[str,str],Tuple[str,str,bool],Sequence[Tuple[str,str]],Sequence[Tuple[str,str,bool]]]) – Single tuple (sample, bam[, is_paired]) or list of tuples.gtf (
str) – GTF annotation file.output_dir (
str(default:'counts')) – Output directory for count files.threads (
int(default:8)) – Threads per featureCounts job.max_workers (
Optional[int] (default:None)) – Legacy alias for jobs.simple (
bool(default:True)) – Simplify output to gene_id + counts.merge_matrix (
bool(default:True)) – Merge per-sample count files into a single CSV matrix (multiple samples only).quiet (
bool(default:True)) – Suppress featureCounts command output.gene_mapping (
bool(default:False)) – Map gene_id to gene_name when exporting simplified counts/matrix.gene_map (
Union[Mapping[str,str],str,None] (default:None)) – Optional mapping dict or file (TSV/CSV or GTF) for gene_id -> gene_name.gene_name_field (
str(default:'gene_name')) – Attribute name in GTF for gene name (default: gene_name).overwrite (
bool(default:False)) – If True, rerun featureCounts and regenerate outputs even if files exist.featurecounts_path (
Optional[str] (default:None)) – Explicit path to featureCounts.auto_install (
bool(default:True)) – Install missing tools automatically when possible.strict (
bool(default:False)) – If True, raise errors; otherwise return error messages per sample.auto_fix (
bool(default:True)) – If True, attempt simple retries (e.g. rerun without paired flags).
- Return type: