It is a small python program to compute alien index, create a report table and analyse that. So you can use it, modify it etc !
To generate the good report, you can use a similar command line :
diamond blastp --db nr_db --threads 32 -q ./proteins_file --out report_blast.tsv --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send slen evalue bitscore sskingdoms sphylums sscinames staxids skingdoms salltitles -e 0.0001 --ultra-sensitive --max-target-seqs 800
Then, you have to generate the lis_id_prot_fungi_uniq
file :
awk -F "\t" '{print $1}' report_blast.tsv | sort| uniq > lis_id_prot_fungi_uniq
sort -k1 report_blast.tsv > report_blast_sorted.tsv
Finally :
Alien_index_report_generator --report /abspath/report_blast_sorted.tsv --id /abspath/lis_id_prot_fungi_uniq --kingdom Fungi
The different kingdom which can be used by this file are :
-
Fungi
-
Viridiplantae
-
Bacteria (This kingdom brings together archaea and bacteria. You have to write 0 (zero) in the command line)
-
Metazoa