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biocommons
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biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
Apache License 2.0
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35
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Ensembl transcript ENST00000617537.5 sequence is wrong (88x larger than it should be)
#170
davmlaw
opened
17 hours ago
0
Concurrent requests to Seqrepo results in sequences being unavailable.
#169
wlymanambry
closed
1 week ago
1
build: update yoyo, setuptools pin no longer needed
#168
jsstevenson
closed
1 month ago
2
chore: remove unused YAPF config
#167
jsstevenson
closed
1 month ago
0
Fail to fetch-load RefSeq sequences
#166
gromdimon
opened
1 month ago
0
chore: add git ignore revs file
#165
jsstevenson
closed
3 months ago
0
refactor: use Python 3 stdlib instead of six
#164
jsstevenson
closed
3 months ago
0
build!: move ipython/repl functionality to optional dependency group
#163
jsstevenson
closed
2 months ago
0
Remove all uses of `six`
#162
jsstevenson
closed
3 months ago
0
refactor: resolve timezone-related python 3.12 deprecations
#161
jsstevenson
closed
1 month ago
3
fix: properly initialize file handler
#160
jsstevenson
closed
3 months ago
0
FabgzWriter file handler property is improperly initialized
#159
jsstevenson
closed
3 months ago
0
style: format with Ruff
#158
jsstevenson
closed
3 months ago
0
docs: add note about commit()
#157
jsstevenson
closed
3 months ago
0
`store()` isn't durably storing sequences
#156
jsstevenson
closed
3 months ago
1
build: require python>=3.10
#155
jsstevenson
closed
2 months ago
2
chore: fix license classifier
#154
jsstevenson
closed
3 months ago
0
fix: remove unneeded __future__ imports
#153
jsstevenson
closed
3 months ago
0
docs: add description of store()
#152
jsstevenson
closed
4 months ago
0
fix: resolve type errors/add type annotations
#151
jsstevenson
closed
4 months ago
0
Reintroduce or remove DuplicateFilter
#150
jsstevenson
opened
4 months ago
1
refactor: use importlib instead of pkg_resources
#149
jsstevenson
closed
4 months ago
0
style: add ruff formatting + linting
#148
jsstevenson
closed
2 months ago
2
IPython dependency -- remove it or make it optional
#147
jsstevenson
closed
2 months ago
1
`seqrepo pull` expects existing `seqrepo` dir
#146
jsstevenson
opened
5 months ago
0
ModuleNotFoundError (pkg_resources) on import in 3.12
#145
jsstevenson
closed
3 months ago
1
Do not preserve permissions when pulling an instance with rsync
#144
theferrit32
closed
5 months ago
0
pre-commit hook causes unexpected problems on existing codebase
#143
theferrit32
closed
3 months ago
2
seqrepo pull often fails when renaming tmpdir
#142
theferrit32
closed
5 months ago
0
style: apply updated style configs from template
#141
jsstevenson
closed
6 months ago
0
--update-latest CLI flag is not pulling in the most recent version
#140
quinnwai
closed
7 months ago
4
fix: finish migrating from setup.cfg to pyproject.toml in order to install seqrepo cli
#139
reece
closed
7 months ago
1
`seqrepo` cli not installed in 0.6.6 and 0.6.7
#138
reece
closed
7 months ago
4
Command Line usage example commands do not run properly
#137
yxuil
opened
7 months ago
3
Generalize the seqrepo interface and implement new backends
#136
reece
opened
7 months ago
5
Problem with latest release (aliases) ...
#134
andreasprlic
closed
7 months ago
2
build: fix dynamic dependencies for newer setuptools versions
#133
jsstevenson
closed
8 months ago
2
Support custom/federated data
#132
jsstevenson
closed
7 months ago
3
feat(130): Introduces SEQREPO_FD_CACHE_MAXSIZE env var
#131
kazmiekr
closed
8 months ago
1
Make fd_cache_size configureable via env variable
#130
andreasprlic
closed
8 months ago
0
Seqrepo not giving back consistent data
#129
wlymanambry
opened
9 months ago
6
Repeated sequence not being captured entirely, intermittent data issues
#128
wlymanambry
opened
9 months ago
1
Sqlite3 timestamp converter is deprecated as of Python 3.12
#127
jsstevenson
closed
1 month ago
1
Database file problem with 2023-09-18 snapshot
#126
ehclark
closed
7 months ago
6
Specify black version
#125
theferrit32
closed
5 months ago
5
Add shell script for autoupdate seqrepo
#124
icebert
opened
1 year ago
2
Citation file
#123
afrubin
closed
1 year ago
0
Update README to support OSX users
#122
dylan-myome
closed
1 year ago
0
Update README to include OSX-facing instructions
#121
dylan-myome
closed
1 year ago
1
#119: migrate to biocommons.example template
#120
reece
closed
1 year ago
0
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