tidesurf.transcript.TranscriptIndex

class tidesurf.transcript.TranscriptIndex(gtf_file: str)

Bases: object

An index of transcripts from a GTF file. Allows for quick retrieval of transcripts on a particular chromosome and strand.

Parameters:

gtf_file str

Path to GTF file.

Attributes

transcripts	Dictionary of transcripts by ID.
transcripts_by_region	Dictionary of transcript intervals by chromosome and strand.

Methods

get_overlapping_transcripts(chromosome, ...)	Get transcripts that overlap with a given region.
get_transcript(self, transcript_id)	Get a transcript by its ID.
read_gtf(gtf_file)	Read a GTF file and construct an index of transcripts.