Python package for Jorge´s JS visualization
usage:
Usage: main.py [mode]
Modes: -B for blast analysis using a query sequence
usage: main.py -B <protein_sequence.fasta> <identity_cut-off>
-E to retrieve all sequence from query Eggnog
usage: main.py -E
For blast analysis its neccesary to get acces to Progenomes blast dabase at: /home/giner/Progenomes_fr11/blast_e5DB
File outputs will be save at /tmp folder:
genes_coordinataes.csv (neighbourhood gene coordinates to plot in JS, not sorted respect to center gene in positive orientation) genes_coordinataes_sorted.csv (neighbourhood gene coordinates sorted respect to center gene in positive orientation) protein_sequence.fasta (query fasta protein of blast) result_blast.tsv (result of blast in table format, HEADER: query_sequence_header;subject_sequence_name;identity;e-value;bit score;coverage;subject seq protein) tree.nwx (EGGnog tree in newick format)