Skip to content
Generates table of blast hits
Python
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
README.md
blastable.py

README.md

blastable

Generates tables of blast hits.

Note: The default threshold is 60% average sequence identity of the alignment divided by the length of the query.

thresh = ((pident*HSPlength)/qlen)

Example usage

python blastable.py -i multifasta.fa ../genomes/

To display other options:

python blastable.py -h

Input File Requirements

The slightly tricky bit is formatting your multifasta.fa headers to be compatible with BLAST.

Each fasta header must contain 2 comma separated fields.

>field1,field2

  • field1 = Gene name (must be unique)
  • field2 = Description (free text, no commas please)

Before the query fasta file can be used with blastable.py:

  1. All spaces should to be replaced with _ (underscore)

Software Dependencies

  1. Command line BLAST on your $PATH
  2. Biopython
  3. Pandas - Python library for data analysis

You can use pip, a python package manager, to install pandas

sudo pip install pandas

Version History

  • v0.1 - Initial version
  • v0.2 - Sorts blast results based on the input sequence. (28 Sep 2015)
  • v0.3 - Handles empty columns. I.e. Queries with no hits in any of the genomes (28 Sep 2015).
  • v0.4 - Prints BLAST results into a separate folder within the working directory. (28 Sep 2015)
  • v0.5 - Also performs blastp. Removed seqfindr format requirement (17 May 2018)
You can’t perform that action at this time.