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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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Deduplication of operons
#163
jimrybarski
closed
3 years ago
0
Temporarily disable property-based tests
#162
jimrybarski
closed
3 years ago
0
Remove redundant operons by seq
#161
jimrybarski
closed
3 years ago
0
Fix blastn strand
#160
jimrybarski
closed
3 years ago
0
Provide access to an operon's nucleotide sequence
#159
jimrybarski
closed
3 years ago
0
Add nucleotide BLAST step
#158
jimrybarski
closed
3 years ago
0
Fix blast type bug
#157
jimrybarski
closed
3 years ago
0
truncate cluster names for really long operons
#156
alexismhill3
closed
3 years ago
2
Allow diagram line wrapping
#155
alexismhill3
closed
3 years ago
0
Make contains_group() case-insensitive
#154
jimrybarski
closed
4 years ago
0
Fix bug that may cause _contains_group to return False prematurely
#153
alexismhill3
closed
4 years ago
0
Prevent redundant operons from being loaded
#152
jimrybarski
closed
4 years ago
2
Eliminate redundant operons
#151
jimrybarski
closed
4 years ago
0
directory names for clustered systems with many genes can be longer than the system character limit
#150
alexismhill3
closed
3 years ago
2
`contains_group` should not be case sensitive
#149
jimrybarski
closed
4 years ago
0
Add a missing interface to the contains_group rule
#148
jimrybarski
closed
4 years ago
0
Add a rule to find contiguous groups of features.
#147
jimrybarski
closed
4 years ago
0
Rule for groups of features
#146
jimrybarski
closed
4 years ago
0
Let user define buffer around features when plotting operons
#145
jimrybarski
closed
3 years ago
1
Use sys.float_info.min instead of epsilon
#144
jimrybarski
closed
4 years ago
1
crash when making BLAST-statistic colormap plots
#143
jimrybarski
closed
4 years ago
0
Better color bounds definition
#142
jimrybarski
closed
4 years ago
0
Color stacked plots by BLAST statistic.
#141
jimrybarski
closed
4 years ago
0
Creates the correct directory.
#140
jimrybarski
closed
4 years ago
0
coloring by BLAST statistic in paired plots
#139
jimrybarski
closed
4 years ago
0
Incorrect subdirectory creation
#138
jimrybarski
closed
4 years ago
0
color by BLAST statistic in clustered stacked plots
#137
jimrybarski
closed
4 years ago
0
Provide an option to incrementally write Gene Finder output to disk
#136
alexismhill3
closed
4 years ago
1
stacked clustered plots
#135
jimrybarski
closed
4 years ago
0
Memory efficient operon loading
#134
jimrybarski
closed
4 years ago
0
Make stacked operon figures for clustered operons
#133
jimrybarski
closed
4 years ago
0
Make `assemble_operons()` memory efficient
#132
jimrybarski
closed
4 years ago
0
Reannotation counts
#131
jimrybarski
closed
4 years ago
2
pilercr segfault
#130
jimrybarski
closed
4 years ago
2
Utility to count re-annotation frequencies
#129
jimrybarski
closed
4 years ago
0
Make rules and filters case-insensitive
#128
jimrybarski
closed
4 years ago
0
Dynamically determine stacked figure dimensions
#127
jimrybarski
closed
4 years ago
0
Color features by BLAST values
#126
jimrybarski
closed
4 years ago
1
Set figure size dynamically for stacked operon figures
#125
jimrybarski
closed
4 years ago
0
operon analyzer cleanup
#124
jimrybarski
closed
3 years ago
2
operon comparison plots
#123
jimrybarski
closed
4 years ago
0
Color by BLAST hit quality
#122
jimrybarski
closed
4 years ago
0
Allow Gene Finder to accept arbitrary blast command flags
#121
alexismhill3
closed
4 years ago
0
Allow user to use regular expressions for feature colors.
#120
jimrybarski
closed
4 years ago
0
Fix broken visualization tests
#119
jimrybarski
closed
4 years ago
0
Ignore build artifacts
#118
jimrybarski
closed
4 years ago
0
Plot pairs of related operons with different annotations together
#117
jimrybarski
closed
4 years ago
0
gene finder should be able to accept arbitrary blast command flags
#116
alexismhill3
closed
4 years ago
0
let the feature colors dictionary take regex keys
#115
jimrybarski
closed
4 years ago
1
allow the user to optionally specify a path to the search utility
#114
alexismhill3
closed
3 years ago
2
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