Stuart #2
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Stuart #2
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…ion and though not as clean or neat allows panning of the 3D plots, which is broken in the previous commit.
… only having 12 colours specified)
…oduced by `linkage_cluster`
…ed distances into similarities
…ntation from the clustering wrapper
…er merging of the clusters back to the structure / variant data frame
…r corresponding UniProt ACs
…ed alpha carbons) and implemented better scaling of 3D plot axes
…d implemented this conversion as an optional step in `variant_distances`
Conflicts: main.py Also retained my config file, `config_stuart.txt`.
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Oh and I can do the merge if you like |
stuartmac
assigned stuartmac, biomadeira and tbrittoborges and unassigned stuartmac and biomadeira
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Didn't realise you could only assign one person! |
tbrittoborges
added a commit
that referenced
this pull request
Nov 18, 2015
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Tests passing. |
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Thanks! Ok I'll give that a try and then delete from the branch. Looks like you forgot to fix the config.py... default config on master now points to 'config_stuart.txt'. If you had merged the pull request locally you could fix something like that afterwards with |
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@tbrittoborges For the sake of interest, i did:
So future pulls shouldn't interfere with either of those files! |
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I merge pulled my branch with master before doing this so we're good to auto merge (excluding my config file and associated config.py). It looks big but there are only a few changes to existing code (see end of this comment).
I've been working on variant clustering the past couple of weeks so theres a new file
clustering.pywith all that. If you run the main block it'll create some figures in a folder called 'cluster_figs' (you'll need to create that first - guess I probably should have checked and done that in the code!) Oh and some of the examples use a method called 'mcl_program', which requires you to have the MCL program from http://micans.org/mcl/ on path (maybe just comment those out if you want to try it). I've also used a python MCL package that's on PyPi.I've also added a few utilities to utils for this. My
fractional_to_cartesianfunctions may end up unused but could be removed later if that's the case.I also made Thiago's cool drop redundant columns feature in
merge_tablesoptional to keep some of my code working for now.And a couple of improvements to my uniprot variants function in
to_table.Lastly, my config file and edited config.py shouldn't be merged to master but I'll keep them in my branch.