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code/modelCuration/reportPeroxGenesFromBetaoxidationGPRsInMito.py
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| # 1. read gene compartment from genes.tsv and load model | ||
| # 2. get the reactions in fatty acid oxidation subsystem and mitochondria compartment | ||
| # 3. go through the reactions and check the compartment of each genes in the GPR | ||
| # 4. report the genes that are only expressed in peroxisome | ||
| import csv | ||
| import cobra | ||
| import pandas as pd | ||
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| # load genes.tsv and read info into a dict for genes and their compartments | ||
| with open("../../model/genes.tsv", 'r') as file: | ||
| reader = csv.reader(file, delimiter='\t') | ||
| geneCompDict = {row[0]: row[8] for row in reader} | ||
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| # load model | ||
| model = cobra.io.load_yaml_model('../../model/Human-GEM.yml') | ||
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| # collect reactions from "Fatty acid oxidation" subsystem and in [m] compartment | ||
| subsys = 'Fatty acid oxidation' | ||
| targetComp = {'m'} | ||
| for r in model.reactions: | ||
| if subsys in r.subsystem and targetComp == r.compartments: | ||
| # go through collected reactions find genes that exist only in peroxisome | ||
| for g in r.genes: | ||
| if geneCompDict[g.id] == 'Peroxisome': | ||
| print(f'{r.id} | {g.id} | {r.build_reaction_string(True)} | {r.gene_reaction_rule} | {r.gene_name_reaction_rule}') | ||
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