CapraLab pdbmap issues - Githubissues

CapraLab / pdbmap

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Load Uniparc sequences from RestAPI

#50 ChrisMoth opened 2 months ago
0
Add Alphamissense scores to SQL database

#49 ChrisMoth opened 5 months ago
0
Add MANE cross-references

#48 ChrisMoth opened 6 months ago
1
Replace Bio:pairwise2 with Pairwise Aligner in PDBMapAlignment.py

#47 ChrisMoth opened 1 year ago
0
Cross reference uniprot IDs to ALL Sifts-aligned PDBs, not just PDB IDs from idmapping

#46 ChrisMoth opened 1 year ago
0
Pdbmap complex

#45 ChrisMoth closed 1 year ago
0
Replace sys.exit() across all modules

#44 ChrisMoth opened 2 years ago
0
VEP echo function broken

#43 ChrisMoth opened 2 years ago
0
With PFAM server going away, create domain graphics locally

#42 ChrisMoth opened 2 years ago
0
Streamline Uniprot IdMapping handling to cope with versioned ENST0000*.N transcript IDs

#41 ChrisMoth opened 2 years ago
0
Move pathprox "complex" code to PDBMapComplex.py Sort out bugs in complex processing

#40 ChrisMoth opened 2 years ago
0
Integrate new Gnomad Mitochondrial data

#39 ChrisMoth opened 2 years ago
0
SIFTS and PDB related database must have case insensitive chain designations

#38 ChrisMoth opened 2 years ago
0
Tolerate abbreviated vcf files

#37 ChrisMoth closed 2 years ago
0
Change Uniparc schema for better MariaDB compatability; Add human-only table

#36 ChrisMoth closed 2 years ago
0
Make VCF parser compatible with ENSEMBL VEP format, 4 column only, vcf files.

#35 ChrisMoth closed 2 years ago
0
VEP command line should not have hard coded version 100

#34 ChrisMoth opened 2 years ago
0
Convert PyVCF lib to Python3, and integrate into PDBMap.

#33 ChrisMoth opened 2 years ago
0
Gnomad Variants: Identify and reject transcripts which don't map to Chrom1-22/X/Y/MT

#32 ChrisMoth opened 2 years ago
0
Style Code to match PEP 8

#31 ChrisMoth opened 2 years ago
0
Alphafold improvements

#30 ChrisMoth closed 2 years ago
0
Inquiry on the Usage

#29 JustinaXie closed 2 years ago
3
Development

#28 ChrisMoth closed 3 years ago
0
Add AlphaFold library module #26

#27 ChrisMoth closed 3 years ago
0
Integrate AlphaFold2 Model support

#26 ChrisMoth closed 2 years ago
0
Document pdbmap.py --load_vcf; comment .slurm scripts

#25 ChrisMoth opened 3 years ago
0
Neanderthal fixes

#24 ChrisMoth closed 3 years ago
0
2020 rework reports

#23 ChrisMoth closed 3 years ago
0
Add access to gene ID numbers from uniprot idmapping

#22 ChrisMoth opened 3 years ago
0
Neanderthal fixes

#21 ChrisMoth closed 3 years ago
0
Neanderthal fixes

#20 ChrisMoth closed 3 years ago
0
Handle Selenomethionine

#19 ChrisMoth closed 2 years ago
1
Development

#18 ChrisMoth closed 3 years ago
0
2020 complexes

#17 ChrisMoth closed 3 years ago
0
Create biounits from mmCIF files, in biopython.

#16 ChrisMoth opened 4 years ago
0
VCF file loading: Refactor files, enhance SQL schema, improve performance.

#15 ChrisMoth closed 2 years ago
0
Refactor Transcript handling for complexes; SQL interfaces; globals

#14 ChrisMoth closed 4 years ago
0
Localize SQL calls to a class that automatically opens/closes based on global configuration

#13 ChrisMoth closed 3 years ago
0
Create tests to validate pdbmap installation, enviornment, and basic return values.

#12 ChrisMoth opened 4 years ago
0
Implement Sifts-uniprot-isoform specific alignments and protein chain's 'best uniprot ID'

#11 ChrisMoth closed 2 years ago
0
Refactor PDBMapTranscript into a heirarchy of transcript types

#10 ChrisMoth closed 2 years ago
0
Allow hot-swtiching of EnsEMBL GRCh3[78] genomes and Database versions

#9 ChrisMoth closed 2 years ago
0
Merge python3 again to pick up new idMapping schema and .gtignore

#8 ChrisMoth closed 5 years ago
0
Python3

#7 ChrisMoth closed 5 years ago
0
Build up pdbmap_v14

#6 ChrisMoth closed 2 years ago
0
Port to Python 3

#5 ChrisMoth closed 4 years ago
0
PDBMapAlignment Incomatible with applications

#4 ChrisMoth closed 2 years ago
0
Alignment of modbase and swiss models to transcripts was incorrect in 0.5% fo cases

#3 ChrisMoth closed 2 years ago
0
NM_ refseq IDs were reformatted in .xlsx spreadsheet for case UDN956557

#2 ChrisMoth closed 2 years ago
0
master branch of CaprLab/pdbmap is far behind MikeSivley/pdbmap branch aspackage

#1 ChrisMoth closed 6 years ago
1