scooby.utils.transcriptome¶
Classes¶
Class for managing genes in an isoform-agnostic way, taking |
Functions¶
|
Convert the last gtf section of key/value pairs into a dict. |
Module Contents¶
- class scooby.utils.transcriptome.Transcriptome(gtf_file, use_geneid=False)¶
- genes¶
- use_geneid = False¶
- read_gtf(gtf_file)¶
- bedtool_exon()¶
- bedtool_span()¶
- write_bed_exon(bed_file)¶
- write_bed_span(bed_file)¶
- scooby.utils.transcriptome.gtf_kv(s)¶
Convert the last gtf section of key/value pairs into a dict.
- class scooby.utils.transcriptome.Gene(chrom, strand, kv)¶
Class for managing genes in an isoform-agnostic way, taking the union of exons across isoforms.
- chrom¶
- strand¶
- kv¶
- exons¶
- add_exon(start, end)¶
BED 0-indexing assumed.
- get_exons()¶
- midpoint()¶
- span()¶
- output_slice(seq_start, seq_len, model_stride, span=False, sliced=True)¶