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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)

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Generates table of blast hits

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