sieve

A little bioinformatics command line tool, for filtering and extracting UniProt FASTA sequences from a file.

For more information about the UniProt FASTA format, take a look at the official UniProt guide.

Quickstart

Run the following command to view all the available filtering options:

sieve --help

Installation

• Using conda (recommended)

conda install -c ehatton sieve

• Using pip

  Download the latest wheel file from the releases section and then install with the following pip command:

pip install sieve-1.0.0-py3-none-any.whl

Usage examples

Filter for human sequences (taxonomy id 9606):

sieve uniprot.fasta out.fasta -t 9606

Filter for human sequences with a maximum length of 100:

sieve uniprot.fasta out.fasta -t 9606 -max 100

Filter for human sequences with a length between 50 and 100:

sieve uniprot.fasta out.fasta -t 9606 -min 50 -max 100

Filter for sequences with gene name BRCA1 or BRCA1, reading from stdin and writing to stdout:

sieve - - -g BRCA1 -g BRCA2 < uniprot.fasta > out.fasta

Convert UniProt text format (flatfile) to FASTA format:

sieve uniprot.txt uniprot.fasta

Get help:

sieve --help

The parse_fasta (for UniProt FASTA files) or parse_text functions (for UniProt text files) can also be used in your own python scripts:

from sieve import FastaParser

with open("my_proteins.fasta", "r") as infile:
    for protein in parse_fasta(infile):
        print(protein) # or do your custom filtering here

Requirements

python version 3.6 or above.

May also work with earlier versions of python 3 but this has not been tested.

Built with

• click

Development setup

unittest is used for the test suite. To run tests:

python -m unittest discover

Release History

• 1.0.0
  • First release

Author

Emma Hatton-Ellis – ehattonellis@gmail.com

License

Distributed under the MIT license. See LICENSE for more information.