legume_gene_count

#Codes for trying to calculate the representative genes in legumes.
#python module networkx required

#Code usage:
##Blast each species against itself using blastx (Run BLAST with these parameters -outfmt "6 qseqid sseqid sscinames scomnames staxid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore")

python selfblast_hsp_filter.R blast_file.tsv
python network_gml.py selfblast_output_10hsp_blast_filtered_nodes.csv selfblast_output_10hsp_blast_filtered_edge.csv
python edgelist_generator.py network.gml
Rscript legume_rep_gene_filter.R

#visualisation
python network_generator.py network.gml

#more than one species
#concatenate all the representative genes together in one file.
##Blast all the representatives against themselves using using blastx (Run BLAST with these parameters -outfmt "6 qseqid sseqid sscinames scomnames staxid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore")

python selfblast_hsp_filter.R all_species_blast_file.tsv
python network_gml.py selfblast_output_10hsp_blast_filtered_nodes.csv selfblast_output_10hsp_blast_filtered_edge.csv
python edgelist_generator.py network.gml
Rscript legume_rep_gene_filter.R