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-features_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"

if 1==0:
    pos_seg="seg_coord/AzucenaRS1_chromosome10.bed"
    out="azucena_chr10_all.gff"

if 1==1:
    out="nb_chr10_all.gff"
    pos_seg="seg_coord/IRGSP-1_0_Chr10.bed"

fct.genome_gff(pos_seg,gff,out)