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Nucleotide A.I.

Project description

ntai

ntai stands for nucleotide (nt) artificial intelligence (A.I.). ntai is a small python library for using fasta sequences with artificial intelligence (A.I.).

Currently there are two main modules that will be of use

  1. Codex, and
  2. bedtools

Codex

Codex is a class for hot-encoding fasta sequences into channels and back. Codex is useful because a character in a fasta sequences can encode multiple nucleotides or even random repeats.

bedtools

bedtools is a function exposing the bedtools library to python. This allows users to extract fasta sequences from a reference genome with writing to / reading from files.

fetch

fetch is a module for fetching the necessary data for using ntai. Currently fetch.utils supports the requests for:

  • fetch_hg38 acquires the fasta for hg38 gzipped

  • fetch_exons acquires Gencode Comprehensive v28 exons in bed format

  • fetch_introns acquires Gencode Comprehensive v28 introns in bed format

  • fetch_hg38_chrom_sizes acquires the chromosome sizes for hg38 in tsv format

  • decompress will decompress a .gz file

The function fetch.fetch_files will get all of these files and decompress hg38 in a specified directory.

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