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usadellab
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prot-scriber
Assigns short human readable descriptions to biological sequences or gene families using references. For this, prot-scriber consumes sequence similarity search results in tabular format (Blast or Diamond).
GNU General Public License v3.0
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add Galaxy badge
#49
bgruening
opened
3 months ago
0
Test different performance calculation
#48
asishallab
opened
5 months ago
0
Annotation typo
#47
Hannah-Doerpholz
closed
3 weeks ago
2
Optimisation of generated HRDs
#46
derRiesenOtter
closed
7 months ago
2
Rerun evaluations
#45
asishallab
closed
3 weeks ago
3
Manually check the "universe" word list generated from Pfam-A and Mercator (Mapman Bin) reference annotations
#44
asishallab
closed
3 weeks ago
2
Bug fix for missing first letters of words
#43
derRiesenOtter
closed
8 months ago
0
added new tests to model_funcs.rs that test if the identifer gets fil…
#42
asishallab
closed
9 months ago
0
Evaluation r exclude 35 50
#41
BellaBagautdinova
closed
9 months ago
0
Wrong annotations in prot-scriber
#40
Hannah-Doerpholz
closed
8 months ago
3
Evaluation r exclude 35 50
#39
BellaBagautdinova
closed
9 months ago
1
Evaluation gene families r
#38
BellaBagautdinova
closed
10 months ago
0
Performance evaluation
#37
asishallab
closed
3 weeks ago
1
Final capture replace filtering
#36
asishallab
closed
2 years ago
0
Issues 26 33 34
#35
asishallab
closed
2 years ago
1
Add a command-line option to exclude "unknown protein" or "unknown sequence family" from results
#34
asishallab
closed
2 years ago
1
Consider phrases consisting only of non-informative words "unknown protein" or "unknown family"
#33
asishallab
closed
2 years ago
1
Improve error messages for input parameter panics
#32
coeit
closed
2 years ago
0
Improve error messages' print out
#31
asishallab
closed
2 years ago
1
Generate regular expression for parsing UniRef
#30
asishallab
closed
2 years ago
1
remerge: Sort equal hsp
#29
coeit
closed
2 years ago
0
Add a trailing newline to the output file
#28
coeit
closed
2 years ago
0
Extended number deletion from stitle
#27
asishallab
closed
2 years ago
0
When generating the human readable description only add phrases that have not already been scores.
#26
asishallab
closed
2 years ago
0
feat: sort equal scoring phrases to ensure a consistent outcome
#25
coeit
closed
2 years ago
0
For equally scoring `phrases` find a deterministic mode of selecting one
#24
asishallab
closed
2 years ago
1
Add information on how to generate gene families to the `.about` in `main.rs`
#23
asishallab
closed
2 years ago
1
Implement `TODO` "Do not use more threads than user specified, even if more Blast tables are to be parsed
#22
asishallab
closed
2 years ago
1
Regex matchgroup desc splitter
#21
asishallab
closed
2 years ago
0
Fix memory usage
#20
asishallab
closed
2 years ago
0
Generate hrd refactor
#19
asishallab
closed
2 years ago
0
Cleaned up Hit
#18
asishallab
closed
2 years ago
0
Parallel no mutex
#17
asishallab
closed
2 years ago
0
Use `String` instead of `&str` in module `generate_hrd_associated_funcs.rs`
#16
asishallab
closed
2 years ago
2
Check for empty input vectors and hashmaps in functions of module `generate_hrd_associated_funcs.rs`
#15
asishallab
closed
2 years ago
1
Funcs for generating hrd
#14
Atemia
closed
2 years ago
3
feat: implement output writer
#13
wunderbarr
closed
2 years ago
2
Clean up and improve performance of `generate_HRD_associated_funcs.rs`
#12
asishallab
closed
2 years ago
2
feat: add gene family parser
#11
coeit
closed
2 years ago
0
Remove deprecated code in Hit and related
#10
asishallab
closed
2 years ago
1
Add optional input support
#9
asishallab
closed
2 years ago
2
When the `generate_human_readable_description` function is implemented, connect it with the existing code
#8
asishallab
closed
2 years ago
0
Implement an output-writer that generates the tabular output of prot-scriber
#7
asishallab
closed
2 years ago
0
Write a parser for input files holding biological sequence families
#6
asishallab
closed
2 years ago
1
Handle parsed Blast results for a given query event
#5
asishallab
closed
2 years ago
1
Filter the word-sets (step 1) using an input vector of regular expressions and flag words that should be scored and those that should not be scored. Have as a result a dictionary of all words, where the values are boolean; true means should be scored.
#4
asishallab
closed
2 years ago
0
Aim at minimum length of HRDs
#3
asishallab
closed
2 years ago
1
Generate reference sets
#2
asishallab
closed
2 years ago
4
feat: blacklists
#1
coeit
closed
2 years ago
1