Dictionary linking organisms to their available fasta files and uniprot annotations

The import functions herein are only for loading data specified in the all_organisms dictionary. This means that the uniprot annotation files referred to herein have already been processed and formatted by alphamap.

all_organisms['Rat']

{'fasta_name': 'rat_[10116].fasta',
 'uniprot_name': 'preprocessed_uniprot_rat.csv'}

Function to load fasta file for a selected organism

import_fasta[source]

import_fasta(organism:str)

Import fasta file for the selected organism. This downloads the file from github if not present.

Args: organism (str): Organism for which the fasta file should be imported. Returns: fasta: Fasta file imported by pyteomics 'fasta.IndexedUniProt' for the selected organism.

Function to load uniprot annotations for a selected organism

import_uniprot_annotation[source]

import_uniprot_annotation(organism:str)

Import uniprot annotation file for the selected organism. This downloads the file from github if not present.

Args: organism (str): Organism for which the uniprot annotation should be imported. Returns: pd.DataFrame: Dataframe with the uniprot annotations for the selected organism.