def build_transcript_dictionary(seqs, genes):
transcripts = {}
for gene in genes:
gene = Gene.from_gff_feature(gene)
if gene == None:
print("Could not convert GFFFeature to Gene, skipping")
continue
new_mrnas = []
for mrna in gene['mrna']:
mrna = Mrna.from_gff_feature(mrna)
if mrna == None:
print("Could not convert GFFFeature to Mrna, skipping")
continue
new_mrnas.append(mrna)
gene.children['mrna'] = new_mrnas
if gene.seqid in transcripts:
transcripts[gene.seqid].genes.append(gene)
else:
if gene.seqid in seqs:
transcripts[gene.seqid] = Transcript([gene], seqs[gene.seqid])
else:
print("Gene "+gene.attributes["ID"]+" is on sequence "+gene.seqid+" which does not exist. Skipping...")
return transcripts
def test_from_gff_features_fails(self):
gff_gene = Mock()
gff_gene.type = "asdf"
tran_gene = Gene.from_gff_feature(gff_gene)
self.assertFalse(tran_gene)
def test_from_gff_feature_success(self):
gff_gene = Mock()
gff_gene.type = "gene"
tran_gene = Gene.from_gff_feature(gff_gene)
self.assertTrue(tran_gene)