Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / SACGF/cdot issues and pull requests

#87 - API/Downloadable JSON differences?

Issue - State: closed - Opened by DGMichael about 1 month ago - 3 comments

#86 - Ensembl Tark Data Provider

Issue - State: closed - Opened by davmlaw 2 months ago - 7 comments

#85 - Make a proper release

Issue - State: open - Opened by davmlaw 3 months ago

#84 - FastaSeqFetcher improvements

Issue - State: open - Opened by davmlaw 3 months ago

#83 - Ensembl files missing protein - breaking c_to_p

Issue - State: closed - Opened by davmlaw 3 months ago - 3 comments

#82 - hgvs c_to_p failing with Ensembl transcript

Issue - State: closed - Opened by chubukov 3 months ago - 7 comments

#81 - Method that returns latest data version

Issue - State: open - Opened by davmlaw 3 months ago

#80 - Ensembl 212 release

Issue - State: closed - Opened by davmlaw 4 months ago - 2 comments

#79 - RefSeq missing MT transcripts

Issue - State: closed - Opened by davmlaw 8 months ago - 6 comments

#78 - JSON breaking schema changes

Issue - State: open - Opened by davmlaw 9 months ago - 2 comments

#77 - Document JSON.gz files, and Transcript format

Issue - State: open - Opened by davmlaw 9 months ago

#76 - CDS phase (offset for eg ribo slippage)

Issue - State: open - Opened by holtgrewe 9 months ago - 5 comments

#75 - Clarify _<symbol> entries

Issue - State: closed - Opened by holtgrewe 9 months ago - 1 comment

#74 - fix: mt_gene for GRCh37 ENSEMBL

Pull Request - State: closed - Opened by holtgrewe 9 months ago

#73 - HGNC ID still missing for some chrMT genes in ENSEMBL

Issue - State: closed - Opened by holtgrewe 9 months ago - 5 comments

#72 - Processing of mitochondrial genes RNA genes broken for ENSEMBL

Issue - State: closed - Opened by holtgrewe 9 months ago - 2 comments

#71 - Mane Plus Clinical tags missing from gff.json.gz files

Issue - State: closed - Opened by holtgrewe 9 months ago - 2 comments

#70 - Use Snakemake to build transcripts

Issue - State: open - Opened by davmlaw 9 months ago - 7 comments

#69 - Transcripts from NCBI/Ensembl API

Issue - State: open - Opened by davmlaw 10 months ago

#68 - Ensembl 111

Issue - State: closed - Opened by davmlaw 10 months ago

#67 - HGVS to VCF Output for HGVS nomenclature with Duplication

Issue - State: closed - Opened by Mchhu about 1 year ago - 1 comment

#66 - Properly tag selenoproteins

Issue - State: closed - Opened by holtgrewe about 1 year ago - 2 comments

#65 - fix: adding dependencies to setup.cfg

Pull Request - State: closed - Opened by holtgrewe about 1 year ago - 3 comments

#64 - Split code and data releases?

Issue - State: closed - Opened by holtgrewe about 1 year ago - 5 comments

#63 - Create VEP-compatible releases in CI

Issue - State: open - Opened by holtgrewe about 1 year ago - 1 comment

#62 - Add tests to CI

Issue - State: open - Opened by holtgrewe about 1 year ago

#61 - fix: RefSeq GFF file now uses the key GenBank rather than Genbank (#60)

Pull Request - State: closed - Opened by holtgrewe about 1 year ago - 1 comment

#59 - Note: PRSS2 / HGNC:9483 missing from cdot v0.2.21 GRCh37/RefSeq

Issue - State: closed - Opened by holtgrewe about 1 year ago - 3 comments

#58 - Create release vor VEP110

Issue - State: closed - Opened by holtgrewe about 1 year ago - 1 comment

#57 - "NM_138693.4" json generation error

Issue - State: closed - Opened by ltnetcase about 1 year ago - 4 comments

#56 - Retrieving duplicate exons from UTA for some transcripts

Issue - State: closed - Opened by davmlaw about 1 year ago - 2 comments

#54 - Diff coding coordinates from latest

Issue - State: open - Opened by davmlaw over 1 year ago

#53 - UTA to cdot transcript start/end conversion issue

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment

#52 - Ensembl 110

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment

#51 - Historical GRCh38 refseq

Issue - State: open - Opened by davmlaw over 1 year ago - 3 comments

#50 - Biotype - missing in Ensembl transcripts

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment

#49 - MT not converted to contigs correctly (GRCh37/Ensembl only)

Issue - State: closed - Opened by davmlaw over 1 year ago

#48 - get_tx_exons - return extra fields if possible

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment
Labels: wontfix

#47 - Implement get_alignments_for_region

Issue - State: closed - Opened by davmlaw over 1 year ago - 2 comments

#46 - get_tx_info should properly handle alt_ac and alt_aln_method

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment

#45 - FastaSeqFetcher - handle deletions

Issue - State: closed - Opened by davmlaw over 1 year ago - 2 comments

#44 - Support for non-human species

Issue - State: closed - Opened by davmlaw over 1 year ago

#43 - Contigs not converted to accession numbers properly

Issue - State: closed - Opened by davmlaw over 1 year ago

#42 - Ensembl T2T - CHM13v2 GTF

Issue - State: closed - Opened by davmlaw over 1 year ago

#41 - Support T2T

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment

#40 - Explain file downloads

Issue - State: closed - Opened by holtgrewe over 1 year ago - 4 comments

#39 - Fasta file SeqFetcher implementation

Issue - State: closed - Opened by davmlaw over 1 year ago - 2 comments

#38 - Differing implementation of get_tx_for_region to hgvs one

Issue - State: closed - Opened by holtgrewe over 1 year ago - 3 comments

#37 - Provide python-attrs classes?

Issue - State: open - Opened by holtgrewe over 1 year ago - 1 comment

#36 - Transcript aliases - HGVS using gene names (canonical transcripts) or LRG

Issue - State: open - Opened by davmlaw over 1 year ago - 2 comments

#34 - PyHGVS - no transcript exception isn't great

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment

#32 - Signature of pyvs_transcript.py get_pyhgvs_data inconsistant

Issue - State: closed - Opened by TheMadBug almost 2 years ago - 1 comment

#31 - Upload release gzip files to github

Issue - State: closed - Opened by davmlaw almost 2 years ago

#30 - Store transcript tags

Issue - State: closed - Opened by davmlaw almost 2 years ago - 1 comment

#29 - All json.gz files should have cdot version in the name

Issue - State: closed - Opened by davmlaw about 2 years ago

#28 - Move up/down transcript versions from VariantGrid to cdot

Issue - State: open - Opened by davmlaw about 2 years ago

#27 - cdot responsible for fixing bad HGVS, allow warnings etc

Issue - State: open - Opened by davmlaw about 2 years ago - 5 comments

#26 - Missing RefSeq GRCh37 GFF

Issue - State: closed - Opened by davmlaw about 2 years ago - 1 comment

#25 - GeneInfo currently fails for some records

Issue - State: closed - Opened by davmlaw about 2 years ago

#24 - Runbook to update/create cdot `json.gz` files

Issue - State: closed - Opened by DavidStreid about 2 years ago - 3 comments

#23 - UTA transcript conversion needs to provide cds_start/cds_end for pyhgvs

Issue - State: closed - Opened by davmlaw about 2 years ago - 1 comment

#21 - Implement HGVS data provider method get_similar_transcripts

Issue - State: closed - Opened by davmlaw about 2 years ago - 1 comment

#20 - Implement HGVS data provider method get_gene_info

Issue - State: closed - Opened by davmlaw about 2 years ago - 3 comments

#19 - Implement HGVS data provider method get_acs_for_protein_seq

Issue - State: closed - Opened by davmlaw about 2 years ago - 1 comment

#18 - Transcripts over a position

Issue - State: closed - Opened by davmlaw over 2 years ago - 1 comment

#16 - Add build patch version

Issue - State: open - Opened by davmlaw over 2 years ago - 1 comment

#15 - Bad conversion of UTA cDNA matches

Issue - State: closed - Opened by davmlaw over 2 years ago - 2 comments

#14 - Add protein IDs to genes

Issue - State: closed - Opened by davmlaw over 2 years ago - 5 comments

#13 - Make UTA optional in refseq generation scripts

Issue - State: closed - Opened by davmlaw over 2 years ago - 1 comment

#11 - Added NCBI release 110

Issue - State: closed - Opened by davmlaw over 2 years ago

#10 - Removing transcript accession number.

Pull Request - State: closed - Opened by Akazhiel over 2 years ago - 2 comments

#9 - ENSEMBL g_to_c

Issue - State: closed - Opened by Akazhiel over 2 years ago - 5 comments

#8 - Move pyreference gff_to_json code into cdot

Issue - State: closed - Opened by davmlaw almost 3 years ago

#7 - Use ijson to reduce RAM usage

Issue - State: closed - Opened by davmlaw almost 3 years ago

#6 - Handle alignment gap (CIGAR) mismatches

Issue - State: closed - Opened by davmlaw almost 3 years ago - 1 comment

#5 - Do some benchmarks

Issue - State: open - Opened by davmlaw almost 3 years ago - 3 comments

#4 - Write a REST client

Issue - State: closed - Opened by davmlaw almost 3 years ago

#3 - Create REST service

Issue - State: closed - Opened by davmlaw almost 3 years ago - 1 comment

#2 - Script to combine genome builds

Issue - State: closed - Opened by davmlaw almost 3 years ago

#1 - Get UTA transcripts

Issue - State: closed - Opened by davmlaw almost 3 years ago