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