maranasgroup / SNPeffect

SNPeffect-

This code corresponds to doi: 10.1111/tpj.14746

SNPeffect: identifying functional roles of SNPs using metabolic networks

Input data is stored under data/. main.py makes input files for the GAMS file findSNPs.gms, which (currently) uses CPLEX to identify SNP activities. The following inputs are needed for main.py -

1. under data/

• AllGenotypesInStudy.txt - list of genotypes in the study
• Biomass_Cons_AllGenotypes.txt - relative growth rate of each genotype wrt the reference genotype (conforming to GAMS formatting)
• Biomass_ConsList_AllGenotypes.txt - list of constraints for the above file (conforming to GAMS formatting)

2. under data/gsm/

• smbl_metabolites.txt - list of metabolites in the GSM model
• smbl_reactions.txt - list of reactions in the GSM model
• smbl_reaction_bounds.txt - reaction bounds for reactions in the GSM model
• smbl_sij.txt - stoichiometric matrix from the GSM model
• FVA.txt - FVA results using nutrients from medium.txt
• maxbiomass_pFBA_FVA.txt - FVA results at maximal biomass value, followed by total flux limited to pFBA value at maximal biomass
• Poplar_GPRrxns_090419.txt - tab delimited file, with reactions (column 1) and associated list of genes (column 2, comma delimited)

3. under data/metabolomics/ - stores genotype-specific metabolite levels

4. under data/genomics/ - stores genotype-wise sequence data