def l_genes(o_org, o_contig):
""" creates a small gene set for testing.
returns a list of 4 genes that belongs
to the same contig and the same organism."""
l_genes = []
c = 10
for i, gene_id in enumerate([
"toto",
"tata",
"titi",
"tutu",
"lolo",
"lala",
"lili",
"lulu",
]):
gene = Gene(gene_id)
gene.fill_annotations(c, c + 30, "+", position=i)
gene.fill_parents(o_org, o_contig)
o_contig.addGene(gene)
gene.family = GeneFamily(i, gene_id)
gene.family.addPartition("c-cloud")
l_genes.append(gene)
c += 35
return l_genes
def l_glist(o_org, o_contig):
""" creates a small testing context, with 4 CDS, 1 RNA that are all on the same contig in the same organism"""
l_glist = []
c = 10
for i, gene_id in enumerate(["toto", "tata", "titi", "tutu"]):
gene = Gene(gene_id)
gene.fill_annotations(c, c + 30, "+", position=i)
gene.fill_parents(o_org, o_contig)
o_contig.addGene(gene)
gene.family = gene_id
l_glist.append(gene)
c += 35
return l_glist