Farm_blast

Run blast+ or blastall in parallel on an LSF compute farm.

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Contents

• Introduction
• Installation
  • Required dependencies
  • Optional dependencies
  • Using pip
  • Running the tests
• Usage
• License
• Feedback/Issues

Introduction

Python3 module to run blast+ or blastall in parallel on an LSF compute farm.

Installation

Farm_blast has the following dependencies:

Required dependencies

• blast+
• fastaq

Optional dependencies

• blastall

Details for installing Farm_blast are provided below. If you encounter an issue when installing Farm_blast please contact your local system administrator. If you encounter a bug please log it here or email us at path-help@sanger.ac.uk.

Using pip

pip3 install farm_blast

Running the tests

The test can be run from the top level directory:
python3 setup.py test

Usage

Compare a query and a reference using blast+ blastn:

farm_blast reference.fasta query.fasta

Compare a query and a reference using blastall blastn:

farm_blast --blastall reference.fasta query.fasta

Run blast+ megablast:

farm_blast --blast_type megablast reference.fasta query.fasta

Run blastall tblastx:

farm_blast --blast_type tblastx --blastall reference.fasta query.fasta

Set the e-value and word length and do not filter the query sequence:

farm_blast --no_filter -e 0.1 -W 30 reference.fasta query.fasta

To get all the options, use --help:

farm_blast --help

License

Farm_blast is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues to the issues page