Metadata-Version: 2.1
Name: upfp
Version: 0.0.3
Summary: UPFP, a package to parse UniProt FASTA files.
Home-page: https://github.com/drugilsberg/uniprot_fasta_parser
Author: Matteo Manica
Author-email: drugilsberg@gmail.com
License: MIT
Description: [![Build Status](https://travis-ci.org/drugilsberg/uniprot_fasta_parser.svg?branch=master)](https://travis-ci.org/drugilsberg/uniprot_fasta_parser)
        # uniprot_fasta_parser
        
        UniProt FASTA parser written in pure python.
        
        ## Development setup
        
        Create a `venv`:
        
        ```sh
        python -m venv venv
        ```
        
        Activate it:
        
        ```sh
        source venv/bin/activate
        ```
        
        Install dependencies:
        
        ```sh
        pip install -r requirements.txt
        ```
        
        Install the package in editable mode:
        
        ```sh
        pip install -e .
        ```
        
        Install `jupiter` playground:
        
        ```sh
        pip install jupyter
        ipython kernel install --user --name=uniprot_fasta_parser
        ```
        
        ## Tutorial on converting FASTA sequences into CSV format
        
        Get the latest FASTA from UniProt SwissProt:
        
        ```sh
        wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
        ```
        
        The script `upfp-fasta-to-csv` (installed with `upfp`) can be used.
        
        ```console
        user@host $ upfp-fasta-to-csv -h
        usage: upfp-fasta-to-csv [-h] [-g] [-c CHUNK_SIZE] fasta_filepath csv_filepath
        
        positional arguments:
          fasta_filepath        path to the FASTA file
          csv_filepath          path where to store the CSV file
        
        optional arguments:
          -h, --help            show this help message and exit
          -g, --gzipped         flag to indicate whether the FASTA is gzipped.
                                Defaults to False.
          -c CHUNK_SIZE, --chunk_size CHUNK_SIZE
                                size of the chunks us
        ```
        
        Provide as input the downloaded gzipped FASTA file and convert it to CSV:
        
        ```sh
        upfp-fasta-to-csv uniprot_sprot.fasta.gz /path/to/file.csv -g
        ```
        
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/markdown
