README.md - ncfp

This repository contains code for a script that identifies and writes the corresponding nucleotide sequences for each protein in an input multiple sequence file to be used, for example, in backthreading coding sequences onto protein alignments for phylogenetic analyses. ncfp uses the NCBI accession or UniProt gene name (as appropriate) to identify source nucleotide sequences in the NCBI databases, download them, and write them to a file.

Quickstart: ncfp at the command-line

Providing an input file of protein sequences as <INPUT>.fasta, and writing output to the directory <OUTPUT>, while specifying a user email to NCBI of <EMAIL> will generate two files: <OUTPUT>/ncfp_aa.fasta and <OUTPUT>/ncfp_nt.fasta.

ncfp <INPUT>.fasta <OUTPUT> <EMAIL>

The file <OUTPUT>/ncfp_aa.fasta contains the amino acid sequences for all input proteins for which a corresponding nucleotide coding sequence could be identified, in FASTA format.

The file <OUTPUT>/ncfp_nt.fasta contains nucleotide coding sequences, where they could be found, for all the input proteins, in FASTA format.

Any input protein sequences for which a corresponding nucleotide sequence cannot be recovered, for any reason, are placed in the file <OUTPUT>/skipped.fas.

To find out more about what ncfp can do, try

ncfp --help

at the command-line

Documentation

For more detailed information about ncfp as a program, or using the underlying ncbi_cds_from_protein Python module, please see the stable version documentation at https://ncfp.readthedocs.io/en/stable/

License

Unless otherwise indicated, all code is licensed under the MIT license and subject to the following agreement:

(c) The James Hutton Institute 2017-2019
(c) The University of Strathclyde 2019-2024
Author: Leighton Pritchard

Contact: leighton.pritchard@strath.ac.uk

Address:
Leighton Pritchard,
Strathclyde Institute for Pharmacy and Biomedical Sciences,
Cathedral Street,
Glasgow,
G4 0RE,
Scotland,
UK

The MIT License

Copyright (c) 2017-2019 The James Hutton Institute Copyright (c) 2019-2024 The University of Strathclyde

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.