Complete file import pipeline from EcoCyc to WCM

[ggsun]

This issue will keep track of the remaining issues that need to be resolved to complete the file import pipeline from EcoCyc to WCM that has been kicked off with PR #1065.

As of May 18th, 2021, the issues are:

• Add back TFs that were removed.
• Test all analysis scripts.
• Emit warnings for molecules in reactions whose specifications are missing from the molecule files.
• Add a way to check which rows are being dropped from data files due to missing components.
• Add script to automatically pull latest versions of files from EcoCyc's API.
• Add patch notes for a list of manual changes made while incorporating these files.
• Clean up models/ecoli/analysis/causality_network/build_network.py for improved robustness.
• Incorporate missing compartment IDs to compartments.tsv.
• Add support for multiple proteins being translated from a single RNA through frameshifting (should be implemented in line with how operons are handled).
• Dynamically calculate molecular weights of modified proteins in 2CS.
• Add hardcoded values in reconstruction/ecoli/dataclasses/process/metabolism.py as raw flat files.
• Automatically add complexed versions of enzymes as functional enzymes for each metabolic reaction.
• Remove hardcoded compartment tags from file reconstruction/ecoli/flat/endoRNases.tsv.
• Pull coordinates of oriC and terC directly from EcoCyc (to be added as a separate file that lists non-genomic locales on the chromosome).
• Exclude unused metabolite-compartment pairs from BulkMolecules.
• Remove redundant common_names flat files.
• Check if the genome sequence needs to be updated.