Smlewis/update commons master oct20 #8
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
These tools are for generating the SQL databases required to run MHCEpitopePredictorExternal predictors with the mhc_energy scoreterm.
Added the capability to look directly for the Rosetta database, assuming that this is being run from Rosetta/tools/mhc_energy_tools and there also exists Rosetta/main/database. Also changed os.environ to os.getenv, which returns None instead of crashing if $ROSETTA hasn't been set, and tweaked the error handling. The logic of how to find the file could maybe be cleaner, but this works for now.
The script would search for all alleles, but only the alleles that met the threshold were stored in details. This also disrupted the summary table. Now, all peptide/allele combos have their details stored in details, but we count if the score meets the threshold using meet-thresh.
…. Added rudimentary plotting capabilities.
I moved matplotlib so that it is only imported if plotting is used, to remove this dependency unless needed. Also fixed the help text in score.py.
Peptides in reports were being output in an arbitrary order with incorrect position numbers. This has now been fixed, and should work with repetitive sequences as well.
A bit more stringent error checking when we keep track of the positions in this way. Also, changed the absolute scoring to the log-transformed format 1-log50k(aff) instead of the affinity. Also added a .gitignore that will ignore output files when running the demo script.
db.py now supports two formats of PSSMs: the one from command line psiblast, and the one from NCBI's PSSM viewer output. If the PSSM is not in that format, it will try to process it, outputting a warning along the way.
…tope breaks; forced 'X' to be epitope break in NetMHC
Previously, if a constructor's initializer list included the C++11
initializer list {} synatx, it would encounter the left curly brace
("{") and interpret it as the start of the constructor's body.
Now it is smarter.
Fixing a related problem where template-specialization functions
where the word "template" shows up but isn't immediately
followed by an opening left angle brace ("<").
e.g.
template void somefunc<int>(int a, int b);
Previously the beautifier would process everything
from "template" to the right angle brace as the template
part, and then hand the opening left paren to be interpretted
as a function. This doesn't work in the new scheme, as the opening
left paren needs to be paid attention to in
process_function_preamble_or_variable.
Now, if a non "<" is hit after the word template, then the process_template
function returns.
…hanged flow accordingly
When outputting resfiles with mhc_gen_db.py, you can now specify which resfile command is set as the default, global setting. If none is specified, it will be left blank.
Added the sequence name to the top of the CSV report, and open the file for appending instead of overwriting. If the user forgets to use a '$' over a multi-sequence scoring run, each report will be appended in the same file.
extern "C" {...} is treated like a namespace
extern int foo() { ... } is treated like a function
The extra debugging output that I had commented back in was leading the serialization test pipeline to conclude that all of the files were failing.
This PR massively reshapes the python_cc_reader module as this module is converted to python3.
The directory structure is as follows:
```
tools/
python_cc_reader/
python_cc_reader/
beauty/
code_improvement/
cpp_parser/
external/
inclusion_removal/
library_splitting/
tests/
utility/
```
The rationale for this dirname-within-dirname structure was given on this page:
https://docs.python-guide.org/writing/structure/
At the top level `python_cc_reader`directory live the user-level scripts such as `library_levels.py` and `beautify_changed_files_in_branch.py.` Within the lower level `python_cc_reader/python_cc_reader` directories live the modules that actually do all the heavy lifting.
These scripts are imported by a number of other scripts in the `tools` repository, and I have updated all of these scripts.
My intention is to create this PR as a permanent record of the merge to master which I am going to make immediately after opening this PR. I will merge this to master in the `tools` repository, and then I will be merging a PR in the `main` repository (PR 4590) that updates the `tools` submodule immediately afterwards.
The URL for the antibody numbering converter changed slightly. Update accordingly.
…/fix_antibody_renumber Fix the convert_pdb_to_antibody_numbering_scheme.py script The URL for the antibody numbering converter changed slightly. Update accordingly.
…repo. This may or may not work for the general public, as I think (but am not sure) I was able to yank out the Meiler-lab specific things.
…mmons_master_oct20
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Updates
masterwith a few years of Commons stuff. I'm not sure why it won't --ff-only merge but it's unlikely to be concerning, probably a hygienic mistake in the past.