### GENCODEGenes
This package loads genes from GENCODE GTF/GFF files, groups transcripts by gene,
and provides methods for transcripts, so you can find exon coordinates, CDS
distances and sequences.
### Install
```sh
pip install gencodegenes
```
### Usage
```py
from gencodegenes import Gencode
gencode = Gencode(GTF_PATH)
# full function arguments are Gencode(gtf_path, fasta_path=None, coding_only=True)
# - fasta_path: pass in path to fasta file to get gene transcripts with sequence
# - coding_only: pass in False to include all transcripts, not just protein coding
# get gene by HGNC symbol
gene = gencode['OR5A1']
transcripts = gene.transcripts
canonical = gene.canonical # picks MANE transcript if available, if none named
# as MANE, picks the one tagged as appris_principal
# (or longest CDS if multiple), if none tagged, picks
# the longest protein coding, if none protein coding,
# picks the longest cDNA
gene.start, gene.end, gene.chrom, gene.strand, gene.symbol # other attributes available
# find gene nearest a genomic position, or overlapping a genomic region
gencode.nearest('chr1', 1000000)
gencode.in_region('chr1', 1000000, 2000000)
# and the transcript has a bunch of methods
tx = gene.canonical
tx.in_exons(pos) # check if pos in exons
tx.in_coding_region(pos) # check if pos in CDS
tx.get_coding_distance(pos) # get distance in CDS to CDS start
tx.get_closest_exon(pos) # find exon closest to position
tx.get_position_on_chrom(cds_pos) # convert CDS pos to genomic pos
tx.get_codon_info(pos) # get info about codon for a site
tx.get_codon_number_for_cds_pos(cds_pos) # convert CDS pos to codon number
tx.translate(seq) # translate DNA to AA (if opened with Fasta)
# the transcript also has associated data fields
tx.name # transcript ID
tx.chrom # transcript chromosome
tx.start # transcript start (TSS)
tx.end # transcript end
tx.cds_start # CDS start position
tx.cds_end # CDS end position
tx.type # transcript type e.g. protein_coding
tx.strand # strand (+ or -)
tx.exons # list of exon coordinates
tx.cds # list of CDS coordinates
tx.cds_sequence # get cDNA sequence (if Gencode was opened with fasta)
```
Raw data
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