Fix duplicate metabolites identified by MetaNetX IDs

[JHL-452b]

Main improvements in this PR:

As discussed in #626

• remove mets MAM03684e for being duplicates

• remove rxns MAR09949, MAR11292, MAR11293 for being affected by duplicate mets

• change MetaNetX ID annotations for MAM03226m, MAM02550c, MAM02550e, MAM01421c, MAM01421m, MAM01421e, MAM00719c, MAM00719r, MAM01759c, MAM01759e, MAM02425c, MAM02425e, MAM01677c, MAM00272c, MAM01321c, MAM01321r, MAM01321e, MAM01321l, MAM01060c, MAM01322c, MAM01631m, MAM01824c, MAM01824m, MAM01996c, MAM00382c, MAM02040c, MAM02040g, MAM02040l, MAM02040m, MAM02040n, MAM02040x, MAM02040r, MAM02040e, MAM02144c

• replace mets

old ID	new ID
MAM03684x	MAM02120x
MAM03684m	MAM02120m
MAM03684c	MAM02120c
MAM00759c	MAM01314c

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[haowang-bioinfo]

instead of solving so many conflicts, would suggest to start a fresh PR from latest develop and cherry pick the commits from here, then close this one

[edkerk]

@haowang-bioinfo You mean have 1 commit for each ID that is changed?

[mihai-sysbio]

Instead of re-doing the commits, one can very simply "copy" commits with https://git-scm.com/docs/git-cherry-pick

[mihai-sysbio]

Instead of re-doing the commits, one can very simply "copy" commits with https://git-scm.com/docs/git-cherry-pick

Perhaps it would have been better with more specific/clear instructions on how to proceed. First, it would be good to update the develop branch in your fork of Human-GEM. Then, checkout a new branch from develop. Then you can use the this command to select the 3 commits introduced in this pull request:

git cherry-pick 543c1ba6808035620ef4658182be771e6c076132 5fbc4d47010b38c47ec2005c37fe205fa18409e9 0c28ca2c0e46f5579ed8b57b4510f14116bbdde7

Finally, based on this new branch, a new pull request can be created with the same message and this one.

[JHL-452b]

This is a great help! I can try this method for subsequent PR.

Actually, there are so many mets should be changed in this PR, especially the references of MetaNetX ID. This may be due to the MetaNetX update. So, would we turn to MNX group for some help as discussion in #626?

[feiranl]

Yes, we will wait a little bit until get response from MNX group