Easy Blast Wrapper And Sequence Trimmer

Given n accessions, downloads the fasta for each accession from NCBI, run command-line BLAST on these fastas, and loads the comparison up in ACT, in just one step.

This is just a simple wrapper on bwast so that there is no need to download the sequences from NCBI yourself, and is easier to install.

Running:

./easy_bwast.py -e <your_email> NZ_AP024098.1 NZ_CP022793.1

will download the fasta for both accessions, run blast and load the alignments on ACT, and show this screen to you: . We download accessions with NCBI Entrez, which requires you to specify your email address with each request.

Create the conda env running: conda env create -f environment.yaml. Then just activate the environment to use easy_bwast: conda activate easy_bwast.

$ ./easy_bwast.py -h
usage: easy_bwast.py [-h] -e EMAIL input [input ...]

Wrapper script to run blast and ACT on accessions without needing to download
them.

positional arguments:
  input                 Specify at least 2 accessions with versions (e.g.
                        NZ_AP024098.1, NZ_CP022793.1, etc)

optional arguments:
  -h, --help            show this help message and exit
  -e EMAIL, --email EMAIL
                        NCBI requires you to specify your email address with
                        each request.

• Enable all CLI options from bwast;
• Make bioconda package;