Added options on samnet.py to use only one exp file (for transcriptional respone) and one phos file (for protein weights) instead of multiple files named by commodities.

- Files in the emt_output directory should be the same, but are now named slightly differently (tgfb_fixed_zeb1_snail_network_gamma14_cap_99_Psiquic_5threshmultiComm... instead of fixed_snail_tgfb_zeb1_network_gamma14_cap_99_Psiquic_5threshmultiComm...)

- Deprecated the following options in samnet.py, commented out --mrnaWeights and --hier-cap, and made relevant changes to the rest of the code: --proteinWeights, --treatmentWeights, --tra, --rawTfData. Added options: --proteinWeightsByComm, --treatmentWeightsByComm, --traByComm, --rawTfDataByComm.