semvec/pypi-packages huggingface dataset:
gencodegenes 1.1.6
Package to load genes from GENCODE GTF files
Requires Python: >=3.8


### 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)

```
cmeel-assimp 6.0.2
cmeel distribution for assimp, Open-Asset-Importer-Library Repository
Requires Python: >=3.9

# CMeel assimp

[![PyPI version](https://badge.fury.io/py/cmeel-assimp.svg)](https://pypi.org/project/cmeel-assimp)
[![Release](https://github.com/cmake-wheel/cmeel-assimp/actions/workflows/release.yml/badge.svg)](https://github.com/cmake-wheel/cmeel-assimp/actions/workflows/release.yml)
[![Build Status](https://api.cirrus-ci.com/github/cmake-wheel/cmeel-assimp.svg)](https://cirrus-ci.com/github/cmake-wheel/cmeel-assimp)

[Assimp](https://github.com/assimp/assimp) distribution for cmeel packages.
refidx 1.3.0
Refractive index database
Requires Python: >=3.10
Keywords: refractive index, optics, electromagnetics




# refidx



<!-- start-badges -->

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<!-- start-desc -->

Retrieve the refractive index of a material at a given wavelength
from the [refractiveindex.info](https://refractiveindex.info/) database.

<!-- end-desc -->


See documentation at [benvial.gitlab.io/refidx](https://benvial.gitlab.io/refidx).



<!-- start-cite -->

#  Citing

##  refidx


> B. Vial. refidx: Python package to retrieve the refractive index of material from the refractiveindex.info database. gitlab (2021). https://benvial.gitlab.io/refidx


Bibtex entry

```bibtex
@software{refidx,
  author   = {Vial, Benjamin},
  title    = {\texttt{refidx}: Python package to retrieve the refractive index of material from  the \texttt{refractiveindex.info} database},
  year     = {2021},
  journal  = {gitlab},
  url      = {https://benvial.gitlab.io/refidx},
}
```


##  refractiveindex.info database


> M. N. Polyanskiy. Refractiveindex.info database of optical constants. Sci. Data 11, 94 (2024). https://doi.org/10.1038/s41597-023-02898-2

Bibtex entry

```bibtex
@article{polyanskiy2024,
	title = {Refractiveindex.info database of optical constants},
	volume = {11},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02898-2},
	doi = {10.1038/s41597-023-02898-2},
	number = {1},
	journal = {Scientific Data},
	author = {Polyanskiy, Mikhail N.},
	month = jan,
	year = {2024},
	keywords = {Materials for optics, Optical materials and structures},
	pages = {94},
}

```


<!-- end-cite -->