Orthologs.py - tools to deal with Leo’s orthology pipeline.¶
| Author: | |
|---|---|
| Release: | $Id$ |
| Date: | December 09, 2013 |
| Tags: | Python |
- Orthologs.FilterBDGP(data)¶
remove genes that are
transcripts from BDGP and genes from ENSEMBL.
If only BDGP genes are present, keep them.
- Orthologs.GetGenes(transcripts)¶
from a list of transcripts get genes.
- Orthologs.ReadInterpretation(infile, separator, genome1=None, genome2=None, filter_restrict_genes1={}, filter_restrict_genes2={}, filter_remove_transcripts1={}, filter_remove_transcripts2={}, filter_restrict_transcripts1={}, filter_restrict_transcripts2={})¶
read interpretation file.
- Orthologs.ReadOrphans(infile, separator, genome1=None, genome2=None, filter_restrict_genes1={}, filter_restrict_genes2={}, filter_remove_transcripts1={}, filter_remove_transcripts2={}, filter_restrict_transcripts1={}, filter_restrict_transcripts2={})¶
read interpretation file.
- Orthologs.ClusterOrthologsByGenes(orthologs)¶
cluster orthologs by genes.
if an orthologous cluster contains the same genes in either species, they are merged.
- Orthologs.GetDegeneracy(t1, t2)¶
get degeneracy of orthology assignments.
given are two lists of transcripts. returns a tuple with gene and transcript degeneracy code, respectively.
