omicverse.utils.gtf_to_pair_tsv¶

omicverse.utils.gtf_to_pair_tsv(gtf_path, output_path, gene_id_version=True)[source]¶

Convert GTF file to gene ID mapping pairs TSV format.

Parameters:

gtf_path (str) – Path to input GTF file.
output_path (str) – Path for output TSV file.
gene_id_version (bool) – Whether to keep version numbers in gene IDs.

Returns:

Number of unique genes written to output file.

Return type:

int

Examples

>>> import omicverse as ov
>>> # Convert GTF to mapping pairs
>>> gene_count = ov.utils.gtf_to_pair_tsv('genes.gtf', 'gene_pairs.tsv')
>>> # Use converted file for gene mapping
>>> data = ov.bulk.Matrix_ID_mapping(data, 'gene_pairs.tsv')