vanheeringen-lab/genomepy issues and pull requests

#251 - Warning only when resource cannot be downloaded

Issue - State: open - Opened by mzavolan about 2 months ago

#250 - fix mysql dependency

Pull Request - State: closed - Opened by Maarten-vd-Sande 2 months ago

#249 - genomepy does not work with mysql 9.0

Issue - State: closed - Opened by biobai 2 months ago - 1 comment

#248 - GenomeDownloadError: FTP host not found: ftp.ebi.ac.uk

Issue - State: closed - Opened by mhfzsharmin 4 months ago - 1 comment

#247 - SSL Error Downloading Genome

Issue - State: open - Opened by sojichld 4 months ago

#246 - Add proxy support

Issue - State: open - Opened by Mitmischer 8 months ago

#245 - Genomepy install gets stuck

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

#244 - does not load gtf with chromose information

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

#243 - search command fails with KeyError: 'submitter'

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

#242 - ucsc can now use the EU mirror

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

#241 - Logger

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

#240 - improved handling of older Ensembl releases

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

#239 - UCSC MySQL mirror selection

Issue - State: closed - Opened by gokceneraslan over 1 year ago - 6 comments

#238 - Logger config overrides client logger config

Issue - State: open - Opened by uniqueg over 1 year ago - 6 comments

#237 - Annotation files not set after fetching

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

#236 - exact flag

Pull Request - State: closed - Opened by siebrenf over 1 year ago - 4 comments

#235 - Partial matching for NCBI taxonomy identifiers is not great for automating genome retrieval

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

#234 - add Annotation.attributes()

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

#233 - certificate error when downloading an ensembl plant genome with annotations

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

#232 - URL Not Found for Rest Server

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

#231 - configure cache expiration time

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

#230 - Option to maintain provider cache?

Issue - State: closed - Opened by bricoletc almost 2 years ago - 5 comments

#229 - Update docs.yml

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

#228 - update docs

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

#227 - change flow, explain plugins better

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

#226 - MySQL connection error

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

#225 - instead of throwing gtfToGenePred errors it should tell user that they should be installed, otherwise users will think annotation download is broken

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

#224 - please, allow to fix the version of ensembl!

Issue - State: closed - Opened by antonkulaga about 2 years ago - 5 comments

#223 - CVE-2007-4559 Patch

Pull Request - State: open - Opened by TrellixVulnTeam about 2 years ago

#222 - Update environment.yml

Pull Request - State: closed - Opened by siebrenf about 2 years ago - 1 comment

#221 - cannot install genomepy with conda on arm64 Mac OS X

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

#220 - Update README.md

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

#219 - Tests

Pull Request - State: closed - Opened by siebrenf about 2 years ago - 1 comment

#218 - dont fail when disabling an already disabled plugin

Pull Request - State: closed - Opened by Maarten-vd-Sande about 2 years ago - 2 comments

#217 - Issue with gtfToGenePred

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

#216 - improve search + update docs

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#215 - -p localfile

Issue - State: closed - Opened by davidhoover over 2 years ago - 6 comments

#214 - check all URLs per provider

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

#213 - genomepy fails when downloading from UCSC

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

#212 - improved thread safety

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#211 - switch to pyproject.toml

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#210 - Bugfix: CLI help menu not showing with no arguments

Pull Request - State: closed - Opened by bricoletc over 2 years ago - 1 comment

#209 - fix ensembl urls, retry cache

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#208 - reduce memory usage

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#207 - total genome sizes

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#206 - Feature request: genome sizes

Issue - State: closed - Opened by bricoletc over 2 years ago - 3 comments

#205 - ensemblgenomes database borked

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

#204 - fixed tests

Pull Request - State: closed - Opened by tilschaef over 2 years ago - 2 comments
Labels: concept

#203 - Mitochondrial genome

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

#202 - issue with annotation in 0.12.0

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

#201 - Lengths

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#200 - details of external databases

Issue - State: open - Opened by zhichengwang59 over 2 years ago - 1 comment

#199 - updated blacklist

Pull Request - State: closed - Opened by siebrenf over 2 years ago - 1 comment

#198 - Diskcache

Pull Request - State: closed - Opened by tilschaef almost 3 years ago - 5 comments

#197 - fix docs

Pull Request - State: closed - Opened by siebrenf almost 3 years ago

#196 - version 0.11.1

Pull Request - State: closed - Opened by siebrenf almost 3 years ago

#195 - Ucsc

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

#194 - Refactor asm report

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

#193 - fix header issue with asm_report

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

#192 - Network Error

Issue - State: open - Opened by ChaoXu1997 almost 3 years ago - 1 comment

#191 - release 0.11.0

Pull Request - State: closed - Opened by siebrenf almost 3 years ago

#190 - easier Annotation class input

Pull Request - State: closed - Opened by siebrenf about 3 years ago - 1 comment

#189 - Using Rich for better terminal output

Issue - State: open - Opened by Mr-Milk about 3 years ago - 1 comment

#188 - small suggestions

Pull Request - State: closed - Opened by Maarten-vd-Sande about 3 years ago - 4 comments

#187 - exactly matching NCBI assembly reports

Issue - State: closed - Opened by siebrenf about 3 years ago
Labels: enhancement

#186 - Gimmescan

Pull Request - State: closed - Opened by siebrenf about 3 years ago - 1 comment

#185 - local provider implemented

Pull Request - State: closed - Opened by siebrenf about 3 years ago - 1 comment

#184 - Caching wrapper

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

#183 - Gencode scaffold fix

Pull Request - State: closed - Opened by siebrenf about 3 years ago - 2 comments

#182 - Ensembl to http

Pull Request - State: closed - Opened by siebrenf about 3 years ago - 1 comment

#181 - gencode provider support (with UCSC genomes)

Pull Request - State: closed - Opened by siebrenf about 3 years ago - 1 comment

#180 - better gff3&gtf conversion + docstrings

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

#179 - How to get Dbxref=GeneID:100287102

Issue - State: closed - Opened by schmucr1 over 3 years ago - 4 comments

#178 - Error: no exon in id-IGHV3-64D-2 contains CDS 555851-556197

Issue - State: closed - Opened by schmucr1 over 3 years ago - 2 comments

#177 - Add a citation file.

Issue - State: open - Opened by simonvh over 3 years ago
Labels: enhancement, minor

#176 - DtypeWarning

Issue - State: closed - Opened by siebrenf over 3 years ago
Labels: minor

#175 - zip support for URL provider

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

#174 - fix circular import

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

#173 - Docs

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

#172 - Import of `as_seqdict`

Issue - State: closed - Opened by simonvh over 3 years ago - 9 comments

#171 - use other annotation files

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

#170 - MySQL for UCSC

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

#169 - Spread

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

#168 - fix some Issues

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

#167 - attempt to cache conda on travis

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

#166 - FR genomepy version in readme

Issue - State: closed - Opened by Maarten-vd-Sande over 3 years ago - 2 comments

#165 - improved black & flake8 feedback

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

#164 - caching

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

#163 - Mapping locations (develop branch) doesn't seem to work

Issue - State: closed - Opened by simonvh over 3 years ago - 2 comments
Labels: bug

#162 - slight reorganization of the mygene functionality

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

#161 - Split modules

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

#160 - Refactors

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

#159 - refactor search functions

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

#158 - refactor annotation PR

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

#157 - cli update

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

#156 - simplified online_provider function

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

#155 - annotation class

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

#154 - Filter sequences in the annotation file

Issue - State: closed - Opened by jma1991 over 3 years ago - 2 comments

#153 - genomepy install error

Issue - State: closed - Opened by fgualdr over 3 years ago - 6 comments

#152 - better NCBI index parsing

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

GitHub / vanheeringen-lab/genomepy issues and pull requests