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genomeannotation
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GAG
Generates an NCBI .tbl file of annotations on a genome.
MIT License
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Dbxref - missing DBTag for Interpro accessions
#148
marchoeppner
closed
9 years ago
1
Multiple DBxref tags
#147
marchoeppner
closed
9 years ago
2
GFF3 output is missing header
#146
marchoeppner
closed
9 years ago
1
Allow multiple parent features
#145
marchoeppner
closed
9 years ago
7
Consider adding functional annotations ONLY to CDS features, not mRNAs
#144
bruab
closed
9 years ago
3
Leave out protein_id for tRNAs
#143
bruab
opened
9 years ago
0
Mark genes as partial if they have a partial mRNA
#142
tedsta
closed
10 years ago
0
Add support for tRNA and rRNA features
#141
bruab
closed
10 years ago
3
Sort genes by indices in output
#140
bruab
closed
7 years ago
1
list functionality
#139
tedsta
closed
10 years ago
0
history
#138
smg283
closed
9 years ago
3
load D. mel, insanity ensues
#137
bruab
closed
10 years ago
1
Error when writing to genome.removed.gff
#136
bruab
closed
10 years ago
0
GFFReader crashes if exons/CDSs have annotations
#135
bruab
closed
10 years ago
0
Overlapping Genes
#134
smg283
closed
7 years ago
0
print list of things being influenced by filter
#133
smg283
closed
10 years ago
0
Transfer AED scores from gff to new gff (and maybe to note on table file
#132
smg283
closed
7 years ago
0
Transfer AED scores from gff to new gff (and maybe to note on table file
#131
smg283
closed
10 years ago
0
weirdness from gene/mrna id hints in console
#130
bruab
closed
10 years ago
0
Hatin' on deepcopy again ...
#129
bruab
closed
10 years ago
4
Docs
#128
bruab
closed
10 years ago
0
Printing gene names in .tbl files when missing protein annotation
#127
bruab
closed
7 years ago
2
cds attributes need to stay sorted
#126
bruab
closed
10 years ago
1
Fix all the min stat weirdnesses
#125
tedsta
closed
10 years ago
0
Bug: Printing Dbxref in tbl when there is no Dbxref
#124
smg283
closed
10 years ago
4
Read gene "Name" from gff, write to tbl
#123
bruab
closed
10 years ago
0
Filters -- min_intron_length behavior on 0-value
#122
bruab
closed
10 years ago
0
Filter requests
#121
tedsta
closed
9 years ago
3
option to write "ignored" features to GFF3
#120
smg283
closed
10 years ago
0
correct reading functional annotations from gff
#119
smg283
closed
10 years ago
3
Stats output file?
#118
smg283
closed
10 years ago
0
Stats summary wording
#117
bruab
closed
10 years ago
0
short introns sneaking past us
#116
bruab
closed
10 years ago
1
add "Seq.remove_empty_mrnas" step to "Controller.apply_filters_n_fixes"
#115
bruab
closed
10 years ago
0
Three-column info
#114
bruab
closed
9 years ago
1
add documentation on how to reset remove/flag operations
#113
bruab
closed
10 years ago
1
verify "__ features flagged" output
#112
bruab
closed
10 years ago
1
filter --> remove / flag
#111
bruab
closed
10 years ago
2
Tear it down
#110
bruab
closed
10 years ago
2
write crashes!
#109
bruab
closed
10 years ago
0
Read annotations from table
#108
bruab
closed
10 years ago
0
Trim regions from .bed file
#107
bruab
closed
10 years ago
1
Remove features from list
#106
bruab
closed
10 years ago
4
'view' doesn't apply filters/fixes
#105
bruab
closed
10 years ago
0
exon/cds NoneType madness
#104
tedsta
closed
10 years ago
0
Some way to leave out certain annotations
#103
bruab
closed
9 years ago
1
Write remove.gff
#102
bruab
closed
10 years ago
3
Split length range filters into separate min/max filters
#101
tedsta
closed
10 years ago
1
Validate indices
#100
bruab
closed
10 years ago
1
fix start_stop_codons not showing up in 'info' right away
#99
bruab
closed
10 years ago
1
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