licence: software on GPL3
author: Lannes Romain 2017 Paris

This script is usefull to make blast all against all, which are at posterior filter by coverage as
it reduce considerably the number of alignment to do. 
 
Simply by doing only the necessary alignment. We tested it on 40 000 sequences it show a speed up
almost 4x. We strongly believe that this speed up may increase with the size of the dataset.

for simple command line information you can use python3 blast_AvA_optimised.py -h

this script can use multi process (multiple cpu) but is not yet mpi (multi computers) which is
something that I have in mind to do.

#It is really simple to use:

you first need to create a working directory.

then you can launch it using:

python3 blast_AvA_optimised.py -wd <working_dir> -input <input file format fasta>
-th <number of cpu to use> -output <output_name>

By default it use a coverage threshold of 80%-80% (reciprocal): you can change it with the -cov option

by default it assume that blastp and makeblasdb are in your path you can set the binary path with:
-blastp and -makeblastdb options

by default the output is outfmt 6 qseqid sseqid evalue pident bitscore qstart qend sstart send qlen slen
which you can change with the option -blast_header

#TODO I also plan to add option to make it possible to use on nucleotide sequence.

# TODO Some Documentation