main.py

import Functions as fct

# creates segments and features for the intersect between the graph for chr10 and the gff of IRGSP
intersect_path='/home/nina/annotpangenome/align_genes/intersect_segments-genes_chr10.bed'
#intersect_path='/home/nina/annotpangenome/align_genes/intersect_reel_genes_chr10.bed'
fct.create_seg_feat(intersect_path)

# outputs the gff of the graph for chr10
output_file='new_graph_chr10.gff'
fct.graph_gff(output_file)


gff="new_graph_chr10.gff"

genome = 'ac'

if genome=='ac': # transfer from graph to azucena
    pos_seg="seg_coord/AzucenaRS1_chromosome10.bed"
    #out="azucena_chr10_all.gff"
    out="azucena_chr10.gff"

if genome=='nb': # transfer from graph to nipponbare
    out="nb_chr10_all.gff"
    pos_seg="seg_coord/IRGSP-1_0_Chr10.bed"

# outputs the gff of a genome for the chr10
fct.genome_gff(pos_seg,gff,out)