def main(gff_file,bed_corrected):
gff = Gff(gff_file)
bed = Bed(bed_corrected)
gffLength = gff.__len__()
gff_index = 0
info, before = '',''
fp=open(gff_file+'.modified','w')
for index in range(gffLength):
item = gff.__getitem__(index)
info = item.accn
if item.accn != 'UNDEF':
if item.type == 'gene':
gene_bed = bed.__getitem__(gff_index).__str__().split('\t')[3]
gene_list = gene_bed.split('|')
paralist = item.accn.split(';')
print(gene_bed, paralist)
if len(gene_list) == 1 and len(paralist)==2:
gene1, gene2 = paralist[0].split(',')[0], paralist[1].split(',')[0]
if gene_bed == gene1:
item.__setattr__("accn", paralist[0])
before = paralist[0]
elif gene_bed == gene2:
item.__setattr__("accn", paralist[1])
before = paralist[1]
else:
before = item.accn
else :
before = item.accn
gff_index = gff_index + 1
else:
item.__setattr__("accn",before)
else:
pass
fp.write(str(item)+'\n')
fp.close()
