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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
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5
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Optionally load features with entire name and description
#113
jimrybarski
closed
4 years ago
1
Add an option to use the whole reference protein description as the gene label
#112
alexismhill3
closed
4 years ago
2
109 allow user to seed a run with coordinates and/or a contig id instead of a bait gene
#111
alexismhill3
closed
4 years ago
1
Gene finder should be able to accept blast databases that haven't been custom annotated
#110
alexismhill3
closed
4 years ago
3
Add an alternative "seed step" to Gene Finder that uses coordinates to define a gene neighborhood
#109
alexismhill3
closed
4 years ago
0
Add method to cluster operons by motif and plot their operon figures …
#108
jimrybarski
closed
4 years ago
0
Add operon clustering function
#107
jimrybarski
closed
4 years ago
0
Dynamically adjust figure width so that tick labels don't overlap.
#106
jimrybarski
closed
4 years ago
0
Lets user define default color for operon visualizations.
#105
jimrybarski
closed
4 years ago
0
Update gene finder portion of the README
#104
alexismhill3
closed
3 years ago
0
Opfi should be briefly described in the README
#103
alexismhill3
closed
3 years ago
0
Rename crisposon to Opfi
#102
alexismhill3
closed
4 years ago
0
Allow default color to be assigned by user
#101
jimrybarski
closed
4 years ago
0
Rules should not consider ignored proteins when being evaluated.
#100
jimrybarski
closed
4 years ago
0
Font size in operon figure X ticks is way too big
#99
jimrybarski
closed
4 years ago
0
Overlapped features can't be ignored by bit score?
#98
jimrybarski
closed
4 years ago
1
Rules should not consider ignored proteins
#97
jimrybarski
closed
4 years ago
0
Tidy up pipeline before merging code-freeze
#96
alexismhill3
closed
4 years ago
0
Resolves #71: Use ORF amino acid sequences instead of alignments in output
#95
alexismhill3
closed
4 years ago
0
Merge code freeze into master
#94
jimrybarski
closed
4 years ago
2
Allow some rules to use regular expressions
#93
jimrybarski
closed
4 years ago
0
consistent use of casing
#92
jimrybarski
closed
4 years ago
0
lookup features using regex
#91
jimrybarski
closed
4 years ago
0
Allow user to define custom filter.
#90
jimrybarski
closed
4 years ago
0
Update CI so it keeps working after we merge code-freeze into master
#89
jimrybarski
closed
4 years ago
0
Merge the documentation of the two modules and fully document how to …
#88
jimrybarski
closed
4 years ago
0
accept custom filters
#87
jimrybarski
closed
4 years ago
0
Record contig filename
#86
jimrybarski
closed
4 years ago
0
save filename to operon analyzer csv
#85
jimrybarski
closed
4 years ago
0
End to end test
#84
jimrybarski
closed
4 years ago
0
Switch to yaml.full_load() to avoid a warning message.
#83
jimrybarski
closed
4 years ago
0
Fix issue where BLAST complains that the query is empty
#82
alexismhill3
closed
4 years ago
0
Complete test coverage for operon analyzer
#81
jimrybarski
closed
4 years ago
0
Fix broken CI run and make tests faster
#80
jimrybarski
closed
4 years ago
0
Plot ignored features correctly.
#79
jimrybarski
closed
4 years ago
0
Plot operons correctly if ignored features are included
#78
jimrybarski
closed
4 years ago
0
Take ignored features into account when plotting them
#77
jimrybarski
closed
4 years ago
0
Resolves #61
#76
alexismhill3
closed
4 years ago
0
Resolves #42
#75
alexismhill3
closed
4 years ago
2
e_value was being passed as a float to `subprocess.run` but it needs …
#74
jimrybarski
closed
4 years ago
3
ensure all ORFs end in complete frame
#73
jimrybarski
closed
4 years ago
0
blast command contains errant float
#72
jimrybarski
closed
4 years ago
0
Save the actual ORF sequence in the pipeline output
#71
alexismhill3
closed
4 years ago
0
Ensure good test coverage for operon analyzer
#70
jimrybarski
closed
4 years ago
0
update installer
#69
jimrybarski
closed
4 years ago
0
Create python-package.yml
#68
jimrybarski
closed
4 years ago
0
Add missing dependencies.
#67
jimrybarski
closed
4 years ago
0
Fix incorrect merging of candidate regions by the pipeline
#66
alexismhill3
closed
4 years ago
0
Pipeline should be able to write temporary hit data to a CSV
#65
alexismhill3
closed
3 years ago
0
Add CRISPR repeat count only during visualization.
#64
jimrybarski
closed
4 years ago
0
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