Metadata-Version: 2.1
Name: ncfp
Version: 0.2.0
Summary: ncfp is a script and module that facilitates recovery of nucleotide sequences from NCBI encoding a specified set of input protein sequences
Home-page: http://widdowquinn.github.io/ncfp/
Author: Leighton Pritchard
Author-email: leighton.pritchard@hutton.ac.uk
License: MIT
Download-URL: https://github.com/widdowquinn/ncfp/releases
Description: # 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.
        
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        ## 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`.
        
        ```bash
        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
        
        ```bash
        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 2019-2020
            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) 2019-2020 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.
        
Keywords: genome bioinformatics sequence
Platform: Posix; MacOS X
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: ~=3.5
Description-Content-Type: text/markdown
