ngs_tools.gtf

Submodules

• ngs_tools.gtf.Gtf
• ngs_tools.gtf.GtfEntry
• ngs_tools.gtf.Segment
• ngs_tools.gtf.SegmentCollection

Package Contents

Functions

parse_gtf(→ Generator[GtfEntry.GtfEntry, None, None])	Parse GTF and yield only the specified features as GtfEntry instances.
genes_and_transcripts_from_gtf(→ Tuple[dict, dict])	Parse GTF for gene and transcript information. Also, compute the introns of

ngs_tools.gtf.parse_gtf(gtf_path: str, filter_func: Callable[[GtfEntry.GtfEntry], bool] = lambda entry: ..., show_progress: bool = False) → Generator[GtfEntry.GtfEntry, None, None]

Parse GTF and yield only the specified features as GtfEntry instances.

Parameters:

• gtf_path – path to GTF file

• filter_func – Function that takes a GtfEntry instance and returns True for entries to process and False for entries to ignore. Defaults to no filtering.

• show_progress – Whether to display a progress bar. Defaults to False.

Yields:

GTF entries

ngs_tools.gtf.genes_and_transcripts_from_gtf(gtf_path: str, use_version: bool = False, filter_func: Callable[[GtfEntry.GtfEntry], bool] = lambda entry: ..., show_progress: bool = False) → Tuple[dict, dict]

Parse GTF for gene and transcript information. Also, compute the introns of each transcript.

Parameters:

• gtf_path – path to GTF file

• use_version – whether or not to use gene and transcript versions

• filter_func – Function that takes a GtfEntry instance and returns True for entries to process and False for entries to ignore. Defaults to no filtering.

• show_progress – Whether to display a progress bar. Defaults to False.

Returns:

Dictionary containing gene information Dictionary containing transcript information