CDHITtoFASTA

Extracts CD-Hit clusters which contain reference proteins and stores them in FASTA format.

CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. CD-HIT was originally developed to cluster protein sequences to create reference databases with reduced redundancy and was then extended to support clustering nucleotide sequences and comparing two datasets.

CD-Hit can also be used to cluster sequences and outputs a cluster file (extension .clstr) contains the accessions of clustered sequence from an input FASTA file.

CDHITtoFASTA uses this cluster file to filter input FASTA files by extracting sequences from the file which CD-Hit finds to cluster with reference sequences.

Command Line Interface Overview

$ python ~/PATH_TO_DIR/CDHITtoFASTA -h
usage: CDHITtoFASTA [-h] [-i CLUSTER] [-s FASTA] [-r LIST]

Extracts CD-Hit clusters which contain reference proteins and stores them in
FASTA format.

optional arguments:
  -h, --help            show this help message and exit
  -i CLUSTER, --cluster_file CLUSTER
                        CD-Hit cluster file which provides clustering
                        information.
  -s FASTA, --sequence_file FASTA
                        FASTA file which provides sequences to be extracted.
  -r LIST, --reference_list LIST
                        File of sequence identifiers (one per line) who's CD-
                        HIT clusters should turned into FASTA files.

Dependencies

• Python 2.7, 3.4 or newer
• Python Packages:
  • biopython 1.63
• CD-Hit 4.6 or newer

To install dependancies on UNIX operating systems:

1. Install CD-Hit via Homebrew or Linuxbrew:

   brew install cd-hit
   

2. Install Biopython via pip:

   pip install biopython
   

Licence

BioMagick is open-source and released under MIT License.

The MIT License (MIT)

Copyright (c) 2014 Lee Bergstrand

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
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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
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SOFTWARE.

Authors

Lee Bergstrand