Dependencies
ncbi-blast+, bedtools
Simple run:
1: python GetGeneIDs.py <gene>
2: bash logcollector.sh <reference genome fasta> <protein fasta of gene used in step 1> <y or n for apply length filter> <multiplier for filter>
Batch run:
Functionality to run in batch mode on a collection of reference genomes and protein fastas
Load all reference genomes into ref/
Load all target proteins into prot/
important: all fastas must be in .fa format
bash automate.sh
Results will be placed in a directory beginning with results followed by a timestamp. e.g. results_2018-02-13-11:00:42