openvax/pyensembl issues and pull requests

#308 - How to convert the name such as '128843_chr7_5473to5474_10k' to gene symbol?

Issue - State: open - Opened by Sarah-air about 1 month ago

#307 - Adding Python Interface files

Pull Request - State: open - Opened by akmazian 4 months ago

#306 - Update species.py

Pull Request - State: open - Opened by pamonlan 6 months ago - 1 comment

#305 - Add support for downloading plant species with pyEnsembl

Pull Request - State: closed - Opened by pamonlan 6 months ago - 1 comment

#304 - [New feature] Switching from argparse to click

Issue - State: closed - Opened by akmazian 7 months ago - 1 comment

#303 - [Housekeeping] Explicitly typing all files!

Issue - State: open - Opened by akmazian 7 months ago - 2 comments

#302 - Update README.md

Pull Request - State: closed - Opened by rraadd88 9 months ago - 1 comment

#301 - Remove nose from tests

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

#300 - Remove nose from tests

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

#299 - A couple of errors encountered with version 2.3.0 (but not with 2.2.9) in `collect_all_installed_ensembl_releases` and `Genome.index` functions

Issue - State: closed - Opened by rraadd88 9 months ago - 3 comments

#298 - [new feature] Support more ensembl genome, such as plants and fungi

Issue - State: open - Opened by y9c 9 months ago - 3 comments

#297 - transcript_support_level attr would cause error when containing space.

Issue - State: open - Opened by y9c 9 months ago - 1 comment

#296 - Similar to the list subcommand, a subcommand to list all available release to download is necessary.

Issue - State: open - Opened by y9c 9 months ago

#295 - Release version 2.3.0

Pull Request - State: closed - Opened by y9c 9 months ago - 7 comments

#294 - More build in species support (zebrafish, nematode )

Pull Request - State: closed - Opened by y9c 9 months ago - 3 comments

#293 - Fix dependency chain broken by newer Polars versions

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

#292 - A few updates

Pull Request - State: closed - Opened by rraadd88 10 months ago - 1 comment

#291 - Polars < 0.17.0 required

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

#290 - reformatted code with Black, increased max ensembl release to 110

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

#289 - chore: bump MAX_ENSEMBL_RELEASE to 110

Pull Request - State: closed - Opened by cameronraysmith about 1 year ago - 2 comments

#288 - Update tags

Issue - State: open - Opened by linqigang888 about 1 year ago - 5 comments

#287 - Bump MAX_ENSEMBL_RELEASE to 110?

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

#286 - protein_ids_at_locus() gives incorrect results

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

#285 - bash: pyensembl: command not found

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

#284 - sqlite bug

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

#283 - is it possible to find the nearest feature when there is none at the locus

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

#282 - Add fruit fly to species

Pull Request - State: closed - Opened by iskandr over 1 year ago - 1 comment

#281 - Update species.py

Pull Request - State: closed - Opened by rraadd88 over 1 year ago - 2 comments

#280 - `distance_to_locus` is inf for loci on opposite strands, feature or a bug?

Issue - State: open - Opened by rraadd88 over 1 year ago - 2 comments

#279 - Rust kernel panic on download

Issue - State: closed - Opened by jordan-schneider over 1 year ago - 11 comments

#278 - Add pandas requirement

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

#277 - Add pandas>=1.3.5 as requirement

Pull Request - State: closed - Opened by deto almost 2 years ago - 2 comments

#276 - Downloading breaks due to reliance on deprecated numpy feature

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

#275 - Include requirements.txt in setup.py

Pull Request - State: closed - Opened by galindus almost 2 years ago - 2 comments

#274 - Can't install v2.2.2 using pip -> requirements.txt missing

Issue - State: closed - Opened by Cloufield almost 2 years ago - 2 comments

#273 - Remove pandas dependency

Pull Request - State: closed - Opened by iskandr almost 2 years ago - 1 comment

#272 - Try using Polars to read GTF files

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

#271 - Update ensembl link to download file

Pull Request - State: closed - Opened by pamonlan almost 2 years ago - 2 comments

#270 - gene class should have a method to get its sequence

Issue - State: open - Opened by antonkulaga almost 2 years ago - 4 comments

#269 - Cannot update Ensembl release

Issue - State: open - Opened by DDudka9 about 2 years ago - 6 comments

#268 - only split name of ENSEMBL naming

Pull Request - State: closed - Opened by y9c about 2 years ago - 2 comments

#267 - Cannot Access the coding sequence in specific transcript

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

#266 - Update ensembl_release_versions.py

Pull Request - State: closed - Opened by y9c about 2 years ago - 2 comments

#265 - [How to use with custom data] NCBI human gene model

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

#264 - pip install in conda does not allow for download

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

#263 - Add additional species

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

#262 - fix assembly name in new release for brown_rat

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

#261 - bump ensembl release version

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

#260 - A method for getting length of the overlap between two loci

Issue - State: open - Opened by integratebio almost 3 years ago

#259 - [Software package citation]

Issue - State: open - Opened by damianosmel almost 3 years ago

#258 - Genbank file with feature output for gene?

Issue - State: open - Opened by harijay almost 3 years ago

#257 - Available assemblies

Issue - State: closed - Opened by DDudka9 almost 3 years ago - 7 comments

#256 - Version 1.9.3

Pull Request - State: closed - Opened by timodonnell almost 3 years ago - 1 comment

#255 - Bump MAX_ENSEMBL_RELEASE to 104

Pull Request - State: closed - Opened by timodonnell about 3 years ago

#254 - "genome" was provided but still raise an error

Issue - State: open - Opened by limin321 over 3 years ago

#253 - Fix transcript id

Pull Request - State: closed - Opened by y9c over 3 years ago - 1 comment

#252 - `.complete` method of `Transcript` class return a wrong result for some transcript ids.

Issue - State: open - Opened by y9c over 3 years ago

#251 - How to run pyensembl using multiple threads?

Issue - State: open - Opened by damianosmel over 3 years ago - 1 comment

#250 - How to select mouse database?

Issue - State: open - Opened by Skychou-source over 3 years ago - 1 comment

#249 - Update max ensemble version from 102 -> 103

Pull Request - State: closed - Opened by Jiafi over 3 years ago - 3 comments

#248 - Error when running top_priority_effect() second time in pyramid webapp

Issue - State: open - Opened by pajanne over 3 years ago

#247 - Upping max release: 100 -> 102

Pull Request - State: closed - Opened by julia326 almost 4 years ago - 1 comment

#246 - Retrieve exon sequences?

Issue - State: open - Opened by pavzz94 almost 4 years ago

#245 - Added exon_by_id function call

Pull Request - State: closed - Opened by davidcotter about 4 years ago - 2 comments

#244 - How to get protein annotation for a input genomic position

Issue - State: closed - Opened by damianosmel about 4 years ago - 4 comments

#243 - Only create cache dir for each Ensembl release if necessary

Pull Request - State: closed - Opened by iskandr about 4 years ago - 1 comment

#242 - Ensemble version of transcript in python API?

Issue - State: open - Opened by arogozhnikov about 4 years ago - 3 comments

#241 - Cache directories created for all releases, not just requested release

Issue - State: closed - Opened by dhimmel about 4 years ago - 2 comments

#240 - Max release 100

Pull Request - State: closed - Opened by iskandr about 4 years ago - 1 comment

#239 - No error from improper install

Issue - State: open - Opened by majohn40 about 4 years ago - 1 comment

#238 - Max release 100

Pull Request - State: closed - Opened by mattdoug604 over 4 years ago - 2 comments

#237 - Potential dependency conflicts between pyensembl and numpy

Issue - State: closed - Opened by NeolithEra over 4 years ago - 3 comments

#236 - [Feature Request] Accessing sequences in arbitrary ranges via Genome class

Issue - State: open - Opened by gokceneraslan over 4 years ago

#235 - Does pyensembl cache mirror the upstream file structure?

Issue - State: open - Opened by Hoeze over 4 years ago - 1 comment

#234 - Max release 99

Pull Request - State: closed - Opened by iskandr over 4 years ago - 1 comment

#233 - Missing scaffold genes

Issue - State: open - Opened by gokceneraslan over 4 years ago - 5 comments

#232 - Potential dependency conflicts between pyensembl and numpy

Issue - State: closed - Opened by NeolithEra almost 5 years ago - 3 comments

#231 - Error when checking that transcript is complete in ensembl69

Issue - State: closed - Opened by scottdbrown almost 5 years ago

#230 - Add check .start_codon_complete

Pull Request - State: closed - Opened by scottdbrown almost 5 years ago - 2 comments

#229 - removed asserts in genome and locus

Pull Request - State: closed - Opened by iskandr almost 5 years ago - 1 comment

#228 - Fix URL path generation issues for Windows 10 users.

Pull Request - State: closed - Opened by fabianegli almost 5 years ago - 6 comments

#227 - Dangerous use of "assert"

Issue - State: closed - Opened by fabianegli almost 5 years ago - 1 comment

#226 - Fix chrM / MT normalization

Pull Request - State: closed - Opened by iskandr about 5 years ago - 1 comment

#225 - Incorrect normalization of "chrM" on GRCh38 to "MT"

Issue - State: closed - Opened by iskandr about 5 years ago

#224 - New ensembl versions 96 97

Pull Request - State: closed - Opened by iskandr about 5 years ago

#223 - pyensembl CLI installs wrong genome

Issue - State: open - Opened by iskandr about 5 years ago - 4 comments

#222 - Updated ensembl_release_versions.py

Pull Request - State: closed - Opened by Flosz about 5 years ago - 2 comments

#221 - Difference between transcript.exon_intervals and transcript.exons

Issue - State: open - Opened by ysbioinfo about 5 years ago

#220 - Increase max Ensembl version to the current 95

Pull Request - State: closed - Opened by krassowski over 5 years ago - 4 comments

#219 - Database path should not default to gtf path

Issue - State: open - Opened by edurand over 5 years ago

#218 - $ pyensembl install --species mouse --release 93 error

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

#217 - Unable to download and innstall ensembl data from command line

Issue - State: closed - Opened by novo1 almost 6 years ago - 6 comments

#216 - Implemented comparison on Locus objects

Pull Request - State: closed - Opened by iskandr almost 6 years ago - 4 comments

#215 - Error in returning gene.exons

Issue - State: closed - Opened by abaltsen almost 6 years ago - 2 comments

#214 - Convert TSL to int?

Issue - State: closed - Opened by iskandr about 6 years ago - 2 comments

#213 - removing encrypted values from Travis

Pull Request - State: closed - Opened by iskandr about 6 years ago - 1 comment

#212 - Add transcript_support_level (TSL) field

Pull Request - State: closed - Opened by vladsavelyev about 6 years ago - 16 comments

#211 - Get rid of ensembl id validation

Pull Request - State: closed - Opened by iskandr about 6 years ago - 1 comment

#210 - added exception is_valid_id for yeast

Pull Request - State: closed - Opened by rraadd88 about 6 years ago - 2 comments

#209 - Add an exception for Saccharomyces cerevisiae in `is_valid_ensembl_id(ensembl_id)` function

Issue - State: closed - Opened by rraadd88 about 6 years ago

GitHub / openvax/pyensembl issues and pull requests