def construct_graph(seq_dict, match_dict, threshold=90):
uf = UnionFind(seq_dict)
component_dict = dict()
for match in match_dict.values():
q_seq = seq_dict[match.q_name]
r_seq = seq_dict[match.r_name]
if match.q_global_identity > threshold or match.r_global_identity > threshold:
uf.union(q_seq.name, r_seq.name)
uf.rename_component()
for seq_name in seq_dict.keys():
seq = seq_dict[seq_name]
component_label = uf.component_label[seq_name]
component_size = uf.component_size[component_label]
seq.label['component'] = component_label
component = Component(component_label)
component.add_member(seq)
if component_label in component_dict:
component_dict[component_label].add_member(seq)
else:
component_dict[component_label] = component
return uf, component_dict
def gene_isoform_analysis(ref_gtf, seq_dict):
gene_dict = dict()
transcript_parent = dict()
ref_gtf = pd.read_table(ref_gtf, sep='\t', header=None, low_memory=False)
ref_gtf.columns = [
'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase',
'header'
]
for i, data in ref_gtf.iterrows():
regex = re.match('transcript_id "(\S+)"; gene_id "(\S+)"',
data['header'])
if regex:
transcript_name = regex.group(1)
gene_name = regex.group(2)
seq = seq_dict[transcript_name]
seq.label['gene'] = gene_name
gene = Component(gene_name)
gene.add_member(seq)
if gene_name in gene_dict:
if seq not in gene_dict[gene_name].member:
gene_dict[gene_name].add_member(seq)
else:
gene_dict[gene_name] = gene
return gene_dict
