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Fixes #3 #4

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Merged
alpae merged 1 commit into from
Feb 25, 2025
Merged

Fixes #3 #4

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22 changes: 15 additions & 7 deletions edgehog/init_extant_synteny_graphs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,22 +83,30 @@ def get_representative_hog_for_gene(ham, hogxml_entries):

# Create a feature "synteny" that stores a synteny graph for the current extant genome
def assign_extant_synteny(genome, gene_dict, ham, orient_edges):
graph = nx.Graph(genome = genome)
graph = nx.Graph(genome=genome)
contiguity_dict = dict()
gene_keys = list(gene_dict.keys())
old_contig = gene_keys[0][0]
hogxml_entries = gene_dict[gene_keys[0]]['hogxml_entries']

# find first gene with hogxml_entries, i.e. that is reported in orthoxml
for first, gene_key in enumerate(gene_keys):
if 'hogxml_entries' in gene_dict[gene_key]:
break
else:
raise ValueError('No gene with hogxml_entries found in genome %s' % genome.name)

old_contig = gene_keys[first][0]
hogxml_entries = gene_dict[gene_keys[first]]['hogxml_entries']
old_gene = get_representative_hog_for_gene(ham, hogxml_entries)
graph.add_node(old_gene, **gene_dict[gene_keys[0]], contig = old_contig)
for i in range(1, len(gene_keys)):
graph.add_node(old_gene, **gene_dict[gene_keys[first]], contig=old_contig)
for i in range(first+1, len(gene_keys)):
contig = gene_keys[i][0]
if 'hogxml_entries' in gene_dict[gene_keys[i]]:
hogs_entries = gene_dict[gene_keys[i]]['hogxml_entries']
gene = get_representative_hog_for_gene(ham, hogs_entries)
graph.add_node(gene, **gene_dict[gene_keys[i]], contig = contig)
graph.add_node(gene, **gene_dict[gene_keys[i]], contig=contig)
if contig == old_contig:
# connect genes only if they are on the same contig
graph.add_edge(old_gene, gene, weight=1, unidirectional=0, convergent=0, divergent=0, children = [None], extant_descendants = [None])
graph.add_edge(old_gene, gene, weight=1, unidirectional=0, convergent=0, divergent=0, children=[None], extant_descendants=[None])
if orient_edges:
old_gene_strand = gene_dict[gene_keys[i-1]]['strand']
gene_strand = gene_dict[gene_keys[i]]['strand']
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