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InteracDome #1472

Merged
merged 147 commits into from
Jul 30, 2020
Merged

InteracDome #1472

merged 147 commits into from
Jul 30, 2020

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ekiefl
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@ekiefl ekiefl commented Jul 20, 2020

This PR implements InteracDome into anvi'o.

Starting this early to potentially receive feedback. As things get closer I will add more context :)

ekiefl added 30 commits June 21, 2020 17:19
@ekiefl
Add a docstring to PfamSetup
b4dff87
@ekiefl
Add option to download custom Pfam version
9fa712a
@ekiefl
docstring
e888ef0
@ekiefl
formatting
4a1eec9
@ekiefl
Move ugly garbage into dedicated methods; some formatting
b0f20d2
@ekiefl
offer quick access to HMMER user guide
6b26977
@ekiefl
shitty is not descriptive. I assumed this was garbage output, but it is
70b720a 
THE output
@ekiefl
Create a sort of useful docstring for the parser. Begin new context
71aea68 
`DOMAIN`
@ekiefl
Add different output option to HMMER class
580966d
@ekiefl
Confused design
e0aef6e
@ekiefl
Suggest biopython for HMMER parsing
85e44e7
@ekiefl
Add method for parsing DOMAIN context
c419624
@ekiefl
OMG IM SO ANGRY. I tried for half the day to fix this mess, but in the
2917f7c 
end, I realized the best thing for my sanity is to simply add to the
pile of crap
@ekiefl
add option to skip checking certificate
aabe777
@ekiefl
create anvi-setup-interacdome file
1a99ebc
@ekiefl
formatting
4cc4635
@ekiefl
interacdome module is born
c4baa2e
@ekiefl
add pdb n interacdome data to gitignore
19ec780
@ekiefl
Basic class to read an HMM profile; write basic filter method
9add056
@ekiefl
Add progress and run info to HMMProfiles; Add method to filter PFAMs in
5903313 
SetupInteracdome
@ekiefl
1 method should not do 2 things
9014ba3
@ekiefl
anvi-setup-interacdome will hmmpress the newly filtered hmm
2cdaa60
@ekiefl
Add InteracdomeTableData class to load query and access the data tables
95ae9b0 
of interacdome
@ekiefl
move parameter descriptions to __init__
5cddc46
@ekiefl
birth of anvi-run-interacdome
3fc5dfb
@ekiefl
Beef up args management
b35de12
@ekiefl
Also filter the clans file
b41814a
@ekiefl
Check data file exists in init
cf67612
@ekiefl
Birth of Interacdome class. Everything is in order. Only the process
6bc0a77 
method needs to be written
@ekiefl
We must assume clans txt has no_header, otherwise we misinterpret the
74dc3a4 
first pfam as the column names
ekiefl added 17 commits July 27, 2020 14:54
@ekiefl
document a design flaw
b249722
@ekiefl
Birth of a new flag that will allow appending data from
e4d72d0 
`additional_amino_acid_data` and `additional_nucleotide_data` to the
output of anvi-gen-variability-profile
@ekiefl
Change default of min binding frequency to 0.2
dd5f332
@ekiefl
new function to do multi-index pivots, see comment
aee2e48
@ekiefl
New method for fetching amino_acid_additional_data for multiple genes
a7dcb2e
@ekiefl
additional data is loaded in VariabilitySuper
6399b04
@ekiefl
Make fetching additional_data more robust
88b4b32
@ekiefl
start merge additional data--checkpoint for the day
8d9c0e4
@ekiefl
Non-varying residues were ending up in the table
488d30c
@ekiefl
attaches to last commit
adfd22d
@ekiefl
additional_data are now reported in gen-variability if flag is supplied
7392eb6
@ekiefl
address multi-column name conflict in laziest way possible
13470dc
@ekiefl
Avoid multi-column conflict in gen-variability by prepending stored
330c7c7 
data-keys with LIG_
@ekiefl
Switch to self-hosted figshare files
1e25e69
@ekiefl
Log how many genes are being HMMed upon
b110032
@ekiefl
Alter HMMER driver to allow both standard out and table outputs
7fecbe4
@ekiefl
anvi-run-interacdome, anvi-run-pfams, anvi-run-hmms all work with new
26bb3f5 
HMMER driver changes
@meren
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meren commented Jul 29, 2020

The mother of all PRs,

image

has conflicts with not one, not two, but three files,

image

as it should.

@ekiefl
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ekiefl commented Jul 29, 2020

I think this is ready to merge, but I am tentative because these two issues on master (#1477 @ivagljiva, #1476 @meren) potentially prevent other bugs from revealing themselves during self tests. When you guys get a chance, could you please check these out?

@ivagljiva
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but I am tentative because these two issues on master (#1477 @ivagljiva, #1476 @meren) potentially prevent other bugs from revealing themselves

I will check it this evening :)

@ekiefl
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ekiefl commented Jul 29, 2020

this commit message honestly had me so curious that I had to look up what 'don't mess with the zohan' was referring to :)

Lmao yes it is Adam Sandler's worst film. But they are all his worst film, which is what is so curious about his career. I have no idea why it popped into my brain.

@ekiefl ekiefl merged commit b27955b into master Jul 30, 2020
@ekiefl ekiefl mentioned this pull request Nov 23, 2020
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@ivagljiva ivagljiva ivagljiva left review comments

@meren meren Awaiting requested review from meren

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3 participants
@ekiefl @meren @ivagljiva