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)
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 = Gene name (must be unique)
- field2 = Description (free text, no commas please)
Before the query fasta file can be used with blastable.py:
- All spaces should to be replaced with
You can use pip, a python package manager, to install
sudo pip install pandas
- 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)