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Move pathprox "complex" code to PDBMapComplex.py Sort out bugs in complex processing #40

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ChrisMoth opened this issue Jul 18, 2022 · 0 comments
Open

Move pathprox "complex" code to PDBMapComplex.py Sort out bugs in complex processing #40

ChrisMoth opened this issue Jul 18, 2022 · 0 comments

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@ChrisMoth
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The PDBMapComplex class manages all aspects of assigning transcripts to chains in a biopython multi-chain structure.

It is being lifted from the PathProx code to have more broad applicaiton

See psbadmin #55 (support cosmis and consurf residue colorings)
ChrisMoth added a commit that referenced this issue Jul 18, 2022
@ChrisMoth
Clean up alignment code for readability,modularize checking of necess…
eb9ac18 
…ary keys in MMcif file for alignment #40
ChrisMoth added a commit that referenced this issue Jul 18, 2022
@ChrisMoth
Ensure all possible genomic positions are considered for gnomad loads…
61753f0 
…, even if non-sequential or reversed #40
ChrisMoth added a commit that referenced this issue Jul 18, 2022
@ChrisMoth
Log errors if sfits unable to store all rows of alignment info in SQL…
c562c5d 
…. This would have caught the case-sensitivity problem earlier #40
ChrisMoth added a commit that referenced this issue Aug 10, 2022
@ChrisMoth
Intial checkin, PDBMapComplex code extracted from pathprox3 #40
7758de4
ChrisMoth added a commit that referenced this issue Aug 10, 2022
@ChrisMoth
PDBMapGlobals is a convenient place to set a global exit function #40
a1546e2
ChrisMoth added a commit that referenced this issue Aug 10, 2022
@ChrisMoth
Intial checkin, PDBMapComplex code extracted from pathprox3 #40
57a9ae8
ChrisMoth added a commit that referenced this issue Aug 31, 2022
@ChrisMoth
Factor out "good enough" transcript comparison code and continue PEP …
dd87971 
…8 cleanups #31 #40
ChrisMoth added a commit that referenced this issue Aug 31, 2022
@ChrisMoth
Cleanup imports and integrate unversioned ensembl transcript IDs for …
86e0331 
…cosmis/rate4site lookups #40 #41
ChrisMoth pushed a commit that referenced this issue Sep 4, 2022
Correctly label rate4site scores and colorings and NOT cosmis #40
8f610eb
ChrisMoth pushed a commit that referenced this issue Sep 5, 2022
Fetching clinvar variants requires the unversioned ensembl transcript…
695404e 
… ids #40
ChrisMoth pushed a commit that referenced this issue Sep 14, 2022
Add Cosmis file load #40
c8b50ab
ChrisMoth pushed a commit that referenced this issue Sep 15, 2022
Write alphafold metrics; Handle missing cosmis scores #40
5c586b1
ChrisMoth pushed a commit that referenced this issue Sep 15, 2022
Fix pdb structure_type typos #40
266693d
ChrisMoth pushed a commit that referenced this issue Sep 23, 2022
Search more thoroughly for rate4site scores #40
38e2729
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@ChrisMoth