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all unique reaction combinations added to cyclic pathways #5

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all unique reaction combinations added to cyclic pathways #5

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8 changes: 6 additions & 2 deletions metquest/pathway_assembler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -292,8 +292,12 @@ def _populate_table(rxns, temp_rxn_list_current, currentcolumnidx):
if succmets in pathway_table:
if succmets in metabs_in_cycle:
if succmets in cyclic_pathways:
cyclic_pathways[succmets].update(
{len(reaction_combntn): [list(reaction_combntn)]})
# multiple reaction_combntn sets may exist the metabolite in a column k, check whether cmbnt exists before appending
if not any(set(reaction_combntn) == existing_set for existing_set in cyclic_pathways[succmets].get(len(reaction_combntn), [])):
cyclic_pathways[succmets].setdefault(len(reaction_combntn), []).append(set(reaction_combntn))
# change from .update to .setdefault method
# cyclic_pathways[succmets].update(
# {len(reaction_combntn): [list(reaction_combntn)]})
else:
cyclic_pathways[succmets] = \
{len(reaction_combntn): [list(reaction_combntn)]}
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