Edinburgh-Genome-Foundry DnaChisel issues

Edinburgh-Genome-Foundry / DnaChisel

:pencil2: A versatile DNA sequence optimizer

https://edinburgh-genome-foundry.github.io/DnaChisel/

MIT License

213 stars 38 forks source link

issues

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Update __init__.py to expose AvoidHeterodimerization

#81 maxall41 opened 3 days ago
0
Question: Avoid sequence of codons

#80 kmcgrathgenerate opened 2 weeks ago
5
Avoiding N-length codon sequences

#79 kmcgrathgenerate closed 3 weeks ago
2
Constraints vs Objectives differences

#78 DomML closed 2 months ago
1
Solving "high repeat density" in codon optimized sequences

#77 snayfach closed 2 months ago
2
constraints_text_summary() says AvoidPattern(RepeatedKmerPattern(2, 9)) passed, but it didn't

#76 Lcarey closed 3 months ago
3
Update biotables.py to allow standard ambigious amino acid annotations (X, B, J, Z)

#75 lauraluebbert closed 1 year ago
1
Allow unknown amino acids denoted by 'X' in `reverse_translate` function

#74 lauraluebbert closed 1 year ago
3
fix non-displayed code blocks in README.rst

#73 Zulko closed 1 year ago
0
Add comparison operators to Location object

#72 godotgildor closed 1 year ago
8
Question: No boost for AllowPrimer

#71 jlerman44 opened 1 year ago
1
Issue when importing as of Nov. 28, 2022

#70 nothinginbiology closed 1 year ago
2
Random reverse translation generator

#69 chillwei closed 1 year ago
0
AvoidPattern with regex

#68 deto closed 1 year ago
2
dnachisel not working on AWS Lambda

#67 guzmanvig closed 2 years ago
6
Remove 'RSCU' from documentation

#66 veghp closed 1 year ago
0
Avoid TF sites example does not work

#65 mschmidt75 closed 2 years ago
5
Geneblocks not displaying gene image on optimization report

#64 kelsi-kw closed 2 years ago
2
Make AvoidPattern() accept multiple patterns

#63 chuanshangtingfeng closed 2 years ago
2
Request: use updated codon usage tables

#62 eggrandio opened 2 years ago
13
Fix #60: "strand sometimes no conserved when AvoidPattern is localized"

#61 Zulko closed 2 years ago
2
Issue with AvoidPattern (and potentially other builtin_specifications)

#60 deto closed 2 years ago
14
v3.2.7

#59 veghp closed 3 years ago
1
Report generation broken after geneblocks install

#58 GC-repeat closed 3 years ago
5
DnaChisel CLI - output to genbank not working

#57 GC-repeat closed 2 years ago
2
Feature: Add "use_breach_form" field in "constraints_breaches_dataframe"

#56 andrewshvv opened 3 years ago
3
Error if ~harmonize_rca used in GenBank

#55 veghp closed 3 years ago
11
Feature: Add GC content variance constraint

#54 andrewshvv opened 3 years ago
8
Error if location not specified

#53 veghp closed 2 years ago
1
EnforcePatternOccurence raises IndexError (in some specific parameters)

#52 ghost closed 3 years ago
5
AvoidPattern with biopython FeatureLocation raises AttributeError (in some specific parameters)

#51 ghost closed 3 years ago
11
Uniquify all kmers when include_reverse_complement=False

#50 seanrj-conagen closed 3 years ago
5
Fix a referenced-before-assignment bug in UniquifyAllKmers

#49 sukolsak closed 3 years ago
2
Spelling

#48 jsoref closed 3 years ago
8
avoiding repeats

#47 aaroncooper closed 3 years ago
2
Custom Codon Usage tables for Codon Optimization

#46 eggrandio closed 3 years ago
2
Avoid repeats in nucleotide sequence

#45 lebolo closed 3 years ago
3
Mismatched amino acid sequence

#44 droidXrobot closed 3 years ago
2
v3.2.5

#43 veghp closed 3 years ago
1
Biopython v1.78 compatibility

#42 veghp closed 3 years ago
1
Raise an error if the codon usage table is not found for the given taxonomy ID

#41 lebolo closed 3 years ago
2
Updated TF binding site example

#40 veghp closed 3 years ago
1
Sequence diversity in output from CodonOptimize

#39 jlerman44 opened 3 years ago
3
Update biotables.py

#38 rfuisz closed 3 years ago
4
Fix AvoidHairpins to search within last window

#37 NikashS closed 3 years ago
5
Fix parameters parsing (convert to str)

#36 simone-pignotti closed 4 years ago
2
Fix docs for CodonOptimize's TaxID species in Genbank API

#35 simone-pignotti closed 4 years ago
2
Design mixin

#34 Lix1993 closed 4 years ago
3
Suggestion: rename biotools to tools

#33 Lix1993 opened 4 years ago
1
relative import

#32 Lix1993 closed 4 years ago
2