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openvax
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pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Get rid of INFO log messages about cached local path
#111
iskandr
closed
8 years ago
0
Discordant number of Exons
#110
alec-djinn
closed
9 years ago
2
Organize cache subdirectories by species, reference, annotation source
#109
iskandr
closed
8 years ago
4
Fixes for various issues after the arbitrary GTF PR
#108
tavinathanson
closed
9 years ago
1
Small typo in GenomeSource.cached_fasta_path
#107
iskandr
closed
9 years ago
0
When sequence data is not provided, error gracefully
#106
tavinathanson
closed
9 years ago
2
EnsemblReleaseSource is not used
#105
tavinathanson
closed
9 years ago
1
Install string bugs
#104
tavinathanson
closed
9 years ago
1
Py2 vs. Py3 pickling
#103
tavinathanson
closed
9 years ago
2
Rename the install command
#102
tavinathanson
closed
7 years ago
1
Remove auto-downloading?
#101
tavinathanson
closed
9 years ago
8
Save arbitrary genomes as entities in the DB
#100
tavinathanson
opened
9 years ago
0
Handle arbitrary GTFs and FASTA files, both local and remote
#99
tavinathanson
closed
9 years ago
10
Gene coordinates discrepancies
#98
alec-djinn
closed
9 years ago
1
try to use less disk space
#97
timodonnell
closed
9 years ago
1
Allow a custom cache directory
#96
tavinathanson
closed
6 years ago
7
Two small performance tweaks
#95
timodonnell
closed
9 years ago
1
Bump datacache version
#94
tavinathanson
closed
9 years ago
0
Pull in the latest version of datacache
#93
tavinathanson
closed
9 years ago
0
support querying the reference genome
#92
timodonnell
opened
9 years ago
1
Allow pyensembl to use any DB-API backend
#91
tavinathanson
closed
9 years ago
2
Loading the NCBI36 Ensembl gives an OperationalError
#90
arahuja
opened
9 years ago
1
Better error on missing transcript
#89
iskandr
closed
9 years ago
1
print biotype as part of Transcript and Gene
#88
iskandr
closed
9 years ago
1
Added "gene" property to Transcript objects which gives access to the parent Gene
#87
iskandr
closed
9 years ago
4
added prebuilt EnsemblRelease objects for major human genomes
#86
iskandr
closed
9 years ago
0
TypeError: unhashable type: 'Database'
#85
alec-djinn
closed
9 years ago
2
Routing Exon and Transcript construction through memoized methods
#84
iskandr
closed
9 years ago
6
Make all PyEnsembl objects hashable
#83
iskandr
closed
9 years ago
1
pyensembl index does not have the same effect as deleting all DB files and re-installing
#82
tavinathanson
closed
7 years ago
6
Fix release 79
#81
iskandr
closed
9 years ago
1
Stop manually maintaining lists of biotype categories
#80
iskandr
closed
6 years ago
0
Separate cache subdirectories for each release
#79
iskandr
closed
9 years ago
1
Errors with the latest `pyensembl`
#78
tavinathanson
closed
9 years ago
2
fixed typo in protein_sequence, increased version, increased max Ensembl version to 79
#77
iskandr
closed
9 years ago
0
Rename Locus to Location
#76
iskandr
closed
6 years ago
0
Contig object for chromosomes and unplaced contigs
#75
iskandr
opened
9 years ago
2
Get all exons of a transcript from a single database query
#74
iskandr
opened
9 years ago
0
Rename "contig" argument names to "seqname"
#73
iskandr
opened
9 years ago
0
Rename EnsemblRelease to Ensembl
#72
iskandr
closed
6 years ago
3
Switch from BioPython to skbio
#71
iskandr
closed
9 years ago
3
Generalized ReferenceTranscripts into SequenceData, added protein sequences
#70
iskandr
closed
9 years ago
7
Create small subset of an Ensembl release for testing
#69
iskandr
closed
8 years ago
1
DB for transcripts
#68
iskandr
closed
9 years ago
6
Cleanup tests
#67
iskandr
closed
9 years ago
1
Error while installing because of progressbar...
#66
alec-djinn
closed
9 years ago
5
Cached data causing failed installation
#65
ihodes
closed
9 years ago
0
Message about saving GTF file printed twice
#64
iskandr
closed
9 years ago
1
Make tests run in Python3
#63
timodonnell
closed
9 years ago
1
travis doesn't seem to work for either Python 2 or 3
#62
timodonnell
closed
9 years ago
1
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