main.py

#!/usr/bin/python

# created by Nina Marthe 2023
# licensed under MIT

from Functions import *
from Graph_gff import *

# 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'
create_seg_feat(intersect_path)



# outputs the gff of the graph for chr10
output_file='graph_chr10.gff'
graph_gff(output_file)


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

gff="graph_chr10.gff"
gfa="data/graphs/RiceGraphChr10_cactus.gfa"

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