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wilkelab
/
Opfi
A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
https://opfi.readthedocs.io/
MIT License
21
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5
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Only modify CRISPR array names for visualization
#63
jimrybarski
closed
4 years ago
1
Make operon analyzer use CSV writer to generate output
#62
jimrybarski
closed
4 years ago
0
Pipeline sometimes reports that a candidate is longer than the actual parent contig
#61
alexismhill3
closed
4 years ago
0
Activate CI
#60
jimrybarski
closed
4 years ago
1
CRISPR arrays are being miscounted
#59
jimrybarski
closed
4 years ago
3
Fully test and document optional pipeline setup arguments
#58
alexismhill3
closed
3 years ago
0
Fix bug that led to crash.
#57
jimrybarski
closed
4 years ago
1
Resolves #46
#56
alexismhill3
closed
4 years ago
0
Fix distance calculation bug
#55
jimrybarski
closed
4 years ago
0
add fuzz tests
#54
jimrybarski
closed
4 years ago
0
Make operon analyzer use CSV writer to read/write output
#53
jimrybarski
closed
4 years ago
0
Fix distance finding when multiple copies of the same feature exist
#52
jimrybarski
closed
4 years ago
0
Fix invalid distances
#51
jimrybarski
closed
4 years ago
0
Resolves #43
#50
jimrybarski
closed
4 years ago
0
Resolves #41.
#49
jimrybarski
closed
4 years ago
0
Operon colors
#48
alexismhill3
closed
4 years ago
1
Resolves #44.
#47
jimrybarski
closed
4 years ago
0
Report additional blast alignment metrics in pipeline output
#46
alexismhill3
closed
4 years ago
0
Mark location of unannotated ORFs in the operon
#45
jimrybarski
closed
3 years ago
1
Display the number of CRISPR repeats in an array
#44
jimrybarski
closed
4 years ago
0
pick between overlapping genes by alignment score
#43
jimrybarski
closed
4 years ago
0
Filter by number of genes
#42
jimrybarski
closed
4 years ago
0
Determine why bait proteins aren't always being displayed
#41
jimrybarski
closed
4 years ago
1
Resolves #38.
#40
jimrybarski
closed
4 years ago
0
Resovles #37.
#39
jimrybarski
closed
4 years ago
1
Document all of operon analyzer
#38
jimrybarski
closed
4 years ago
0
Operon analyzer should handle output from multiple pipeline CSVs gracefully
#37
jimrybarski
closed
4 years ago
0
Allow user to choose to display ignored features
#36
jimrybarski
closed
4 years ago
0
Operon analyzer
#35
jimrybarski
closed
4 years ago
0
Multi sequence fasta support
#34
alexismhill3
closed
4 years ago
0
Automatically install wheel if it's not present already during setup
#33
jimrybarski
closed
4 years ago
0
Add an option to toggle writing intermediate hits
#32
alexismhill3
closed
4 years ago
0
Add support for blast alternatives
#31
alexismhill3
closed
4 years ago
0
Document sequence identifier requirements
#30
jimrybarski
closed
3 years ago
2
Add pytest as a dependency
#29
jimrybarski
closed
4 years ago
0
Develop
#28
alexismhill3
closed
4 years ago
1
Add a minimum protein count option to filter step
#27
alexismhill3
closed
4 years ago
0
Add output format as a parameter of pipeline.run()
#26
alexismhill3
closed
4 years ago
0
Cleanup final output
#25
alexismhill3
closed
4 years ago
0
Make the input assembly file a parameter of pipeline.run()
#24
alexismhill3
closed
4 years ago
0
Better annotation of fused genes
#23
alexismhill3
closed
3 years ago
0
Add trailing Ns to second and third nt reading frames so that they are still divisible by 3
#22
alexismhill3
closed
4 years ago
0
More informative and cleaner logging
#21
alexismhill3
closed
3 years ago
0
actually delete the examples folder
#20
alexismhill3
closed
4 years ago
0
rename examples to extras and add additional scripts
#19
alexismhill3
closed
4 years ago
0
Add demo script
#18
alexismhill3
closed
4 years ago
0
Handle early termination of main loop in pipeline.run
#17
alexismhill3
closed
4 years ago
0
Enable small array detection by pilercr
#16
alexismhill3
closed
4 years ago
0
Get local and remote versions synced before deploying on tacc
#15
alexismhill3
closed
4 years ago
0
Integration tests
#14
alexismhill3
closed
3 years ago
0
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