Ecosyste.ms: Issues

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

GitHub / daler/gffutils issues and pull requests

#235 - drop usage of Python2-era simplejson

Pull Request - State: open - Opened by a-detiste 3 months ago

#234 - Trouble with db.region(..., completely_within=True)

Issue - State: open - Opened by Lservi 5 months ago - 1 comment

#233 - test_roundtrip fails: test_roundtrip

Issue - State: open - Opened by yurivict 5 months ago - 1 comment

#232 - Update an entry and retain children

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

#231 - V0.13rc

Pull Request - State: closed - Opened by daler 8 months ago

#230 - Value of Target attribute gains quotes when it shouldn't in round trip manipulation

Issue - State: open - Opened by photocyte 8 months ago - 4 comments
Labels: feature request

#229 - Add pytest 8.x compat

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

#228 - move strand specification to FeatureLocation in `to_seqfeature`

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

#227 - FeatureDB.update on disk db very slow

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

#226 - How to get closest features?

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

#225 - Fix repository URL in README.rst

Pull Request - State: closed - Opened by AMDmi3 11 months ago - 1 comment

#222 - V0.12rc

Pull Request - State: closed - Opened by Juke34 over 1 year ago - 1 comment

#221 - v0.12 rc

Pull Request - State: closed - Opened by daler over 1 year ago - 3 comments

#220 - add a function to create splice sites similar to create_introns

Pull Request - State: closed - Opened by Juke34 over 1 year ago - 4 comments

#219 - Fix bug multiple values for ID attribute are no longer permitted since v0.11

Pull Request - State: closed - Opened by Juke34 over 1 year ago - 3 comments

#218 - How to get all the gene ids of the read gff file

Issue - State: closed - Opened by z626093820 over 1 year ago - 1 comment

#217 - how to save the modified gff to the disk

Issue - State: closed - Opened by z626093820 over 1 year ago - 2 comments

#216 - Sqlite3.OptimizedUnicode deprecation warning

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

#215 - replace base split by regex split to fix ; inside quotes

Pull Request - State: open - Opened by DevangThakkar over 1 year ago - 2 comments

#214 - merge_strategy='create_unique' not always creating unique id's

Issue - State: open - Opened by novigit over 1 year ago - 2 comments
Labels: needs-discussion

#213 - create_db() does not parse directives from GFF files starting in v0.11.0

Issue - State: open - Opened by dtdoering over 1 year ago - 3 comments
Labels: needs-discussion

#212 - Field separators in quoted attributes cause error

Issue - State: open - Opened by zwpwjwtz over 1 year ago - 4 comments
Labels: needs-discussion

#210 - gtf_extract command not found with conda installation

Issue - State: closed - Opened by almart7 almost 2 years ago - 4 comments

#209 - add test for #207

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

#208 - fix #198

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

#207 - Inconsistent behaviour of trailing semicolon

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

#206 - Handling of multi-line features with same ID

Issue - State: closed - Opened by andrewkennard almost 2 years ago - 3 comments

#205 - Apologies - delete me!

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

#204 - db.parents(id) stops at level 2?

Issue - State: open - Opened by dariober almost 2 years ago

#203 - Map transcript coordinates to genome coordinates

Issue - State: open - Opened by dariober almost 2 years ago - 3 comments
Labels: feature request

#202 - "ValueError: The ID field ID has more than one value" when updating database.

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

#201 - Use pytest instead of the Py3.11 incompatible nose (#200)

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

#200 - Use pytest instead of the Py3.11 incompatible nose

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

#199 - fix #197

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

#198 - How to create database for GRCh38_latest_genomic.gtf.gz?

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

#197 - Updating db with intergenic space features

Issue - State: closed - Opened by novigit about 2 years ago - 9 comments

#196 - SyntaxError when importing gffutils using python 2.7.15

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

#194 - Same IDs for gene_id and transcript_id

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

#193 - address #181

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

#192 - address #174 (new numeric_sort arg)

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

#191 - address #167

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

#190 - add new FeatureDb.seqids; addresses #166

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

#189 - address #164

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

#188 - address #159

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

#187 - address #157

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

#186 - Fix docs in 3.8

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

#185 - address #128

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

#183 - Missing docstring entry

Issue - State: closed - Opened by scimerc over 2 years ago - 1 comment
Labels: v0.11

#182 - `id_spec` default can be misleading

Issue - State: closed - Opened by scimerc over 2 years ago - 3 comments
Labels: v0.11

#181 - Import of introns fails

Issue - State: closed - Opened by Yu-jinKim over 2 years ago - 2 comments
Labels: v0.11

#180 - Pep8 cleanup

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

#179 - Refactor iterators

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

#178 - v0.11

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

#177 - move tests from from travis-ci to github actions

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

#176 - Testing actions

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

#175 - target branch for v0.11

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

#174 - Inconsistent Ordering of exon_number attribute in introns

Issue - State: closed - Opened by mbiokyle29 almost 3 years ago - 2 comments
Labels: v0.11

#173 - Feature.sequence misses last base

Issue - State: closed - Opened by kathryncrouch about 3 years ago - 1 comment

#172 - Handle a bug in NCBI gtf

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

#171 - Handle empty string in Quoter

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

#170 - AttributeError: 'FeatureDB' object has no attribute 'strand'

Issue - State: closed - Opened by mictadlo over 3 years ago - 1 comment

#169 - Use Context Manager in FileIterator

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

#168 - Python3 DeprecationWarning: invalid escape sequence \w

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

#167 - create_db sqlite3.InterfaceError (small genome)

Issue - State: closed - Opened by soungalo almost 4 years ago - 3 comments
Labels: v0.11

#166 - How to get all chromsome names and featuretypes

Issue - State: closed - Opened by zhqu1148980644 almost 4 years ago - 1 comment
Labels: v0.11

#165 - Fix deprecation warning.

Pull Request - State: closed - Opened by roryk almost 4 years ago

#164 - Tasmanian devil transcriptome is not loading in the database

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

#163 - sort_attribute_values -- how to keep the exons in numerical order

Issue - State: closed - Opened by Xiaofei-git over 4 years ago - 2 comments

#162 - fixed bug mentioned in issue #129

Pull Request - State: closed - Opened by husensofteng over 4 years ago

#161 - Proper way to sort/order features after merge?

Issue - State: closed - Opened by bbimber over 4 years ago - 2 comments

#160 - Intergenic feature generation

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

#159 - Repair canonical_transcripts

Issue - State: closed - Opened by EFraim over 4 years ago - 2 comments
Labels: v0.11

#158 - Can't get children from NCBI GFF (may be user error)

Issue - State: closed - Opened by deannachurch over 4 years ago - 13 comments

#157 - Bug: New merge method does not have "ignore_strand" argument => merge=True throws error

Issue - State: closed - Opened by sschmeier over 4 years ago - 2 comments
Labels: v0.11

#156 - Repair canonical_transcripts

Pull Request - State: open - Opened by EFraim over 4 years ago

#155 - Avoid deadlocks in tests under Python 3.8

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

#154 - change IDs in a GFF3

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

#153 - Better handling of merged components

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

#152 - Fix major issue with merge algorithm, add new merge criteria (v0.10.1rc)

Pull Request - State: closed - Opened by innovate-invent almost 5 years ago - 5 comments

#151 - much-improved merging (updated version of PR #130)

Pull Request - State: closed - Opened by daler almost 5 years ago

#150 - More issue 119 tests

Pull Request - State: closed - Opened by daler almost 5 years ago

#149 - v0.10rc

Pull Request - State: closed - Opened by daler almost 5 years ago

#148 - Introducing new attributes and values from data file

Issue - State: closed - Opened by igwill almost 5 years ago - 10 comments

#147 - inspect.py vs inspection.py?

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

#146 - creating a file with gene/transcript from exon only lines

Issue - State: closed - Opened by lpantano about 5 years ago - 1 comment

#145 - Ensure that tests work post-installation

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

#144 - 'part' is not defined if val_str is empty

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

#143 - Is it possible to create a db only for one chromosome?

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

#142 - fix for GFFs with ##FASTA section in python 3.7

Pull Request - State: closed - Opened by pbradz about 5 years ago - 3 comments

#141 - No all features are written to file

Issue - State: closed - Opened by mictadlo about 5 years ago - 1 comment

#140 - Id collision resolution broken

Pull Request - State: closed - Opened by abhishekkumaresan over 5 years ago

#139 - Fix interfeatures merge attributes

Pull Request - State: closed - Opened by stekaz over 5 years ago

#137 - Generating New Parent Attributes from gene_ID

Issue - State: closed - Opened by Jome0169 over 5 years ago - 1 comment

#134 - Update conda and pypi

Issue - State: closed - Opened by innovate-invent over 5 years ago - 1 comment

#130 - Improve merge and add merge_all

Pull Request - State: closed - Opened by innovate-invent over 5 years ago - 13 comments

#129 - region() behavior at the feature boundaries

Issue - State: closed - Opened by littleblackfish over 5 years ago - 9 comments
Labels: v0.11