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modernatx
/
seqlike
Unified biological sequence manipulation in Python
https://modernatx.github.io/seqlike
Apache License 2.0
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Fixing the random codon table probabilities
#85
amine-abdeljaoued
opened
5 months ago
0
High Memory Footprint Due to (mostly?) Unused Attribute
#84
Yashrajsinh-Jadeja
opened
6 months ago
3
random_codon_table not random for Isoleucine
#83
amine-abdeljaoued
opened
6 months ago
2
BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
#82
arjan-hada
opened
9 months ago
0
annotations persist after mutation
#81
ndousis
closed
8 months ago
1
loss of SeqRecord.features when applying Mutation
#80
ndousis
closed
8 months ago
0
Failure to import in ipython notebook
#79
mccaron707
opened
9 months ago
0
changed .getsize to .getlength for compatibility with Pillow 10
#78
ndousis
closed
1 year ago
2
AttributeError: 'FreeTypeFont' object has no attribute 'getsize' (Pillow 10)
#77
ndousis
closed
1 year ago
0
fixes #75 by bandaging a python_codon_tables bug
#76
ndousis
closed
1 year ago
1
fix codons_table bug
#75
ndousis
closed
1 year ago
0
fix Biopython deprecation warning for ungap()
#74
ndousis
closed
1 year ago
1
BiopythonDeprecationWarning: myseq.ungap(gap) is deprecated; please use myseq.replace(gap, "") instead
#73
ndousis
closed
1 year ago
0
simplify SeqLike.__getitem__() to ignore the AA sequence when accessing/slicing the NT sequence
#72
ndousis
opened
1 year ago
2
added a sorting function such that deterministic codon map chooses codons by highest frequency
#71
ndousis
closed
1 year ago
2
deterministic codon map by `codon_table_to_codon_map()` effectively chooses codons arbitrarily
#70
ndousis
closed
1 year ago
1
added "DNA" `molecule_type` annotation after back_translation
#69
ndousis
closed
1 year ago
2
`molecule_type` annotation lost in translated-back-translated sequence
#68
ndousis
closed
1 year ago
5
update OneHotEncoder to use sparse_output instead of sparse
#67
ndousis
closed
1 year ago
1
sklearn OneHotEncoder FutureWarning
#66
ndousis
closed
1 year ago
0
docs: add JacobHayes as a contributor for infra
#65
allcontributors[bot]
closed
2 years ago
0
Add missing setup.py deps, add notebook extras, and move test deps to extras
#64
JacobHayes
closed
2 years ago
2
Mutation class #57
#63
ericmjl
closed
1 year ago
6
docs: add farbod-nobar as a contributor for code
#62
allcontributors[bot]
closed
2 years ago
0
Fix weblogo alphabet in SeqLikeAccessor.py
#61
farbod-nobar
closed
2 years ago
1
add commandline wrapper function for Muscle 3.8 #24
#60
ndousis
closed
2 years ago
2
docs: add dmnfarrell as a contributor for code
#59
allcontributors[bot]
closed
2 years ago
0
Adding Damien Farrell as a contributor
#58
ericmjl
closed
2 years ago
4
Objects to represent mutations
#57
ericmjl
closed
1 year ago
6
fixed #51 (Prepending a string to a SeqLike)
#56
ndousis
closed
2 years ago
0
Add lazy-loader to requirements.txt
#55
ericmjl
closed
2 years ago
0
Provide a function in alphabets to test if an alphabet is a super-set of AA/STANDARD_AA
#54
andrewgiessel
closed
2 years ago
1
[ENH] Speed up import time of SeqLike
#53
ericmjl
closed
2 years ago
0
Lazy Imports
#52
ericmjl
closed
2 years ago
0
Prepending a string to a SeqLike
#51
ndousis
closed
2 years ago
3
Feature/create sequence like
#50
andrewgiessel
closed
2 years ago
3
Support arbitrary alphabets
#49
ericmjl
closed
2 years ago
2
Infrastructure-improvements
#48
ericmjl
closed
2 years ago
1
Added conda install info to readme
#47
sugatoray
closed
2 years ago
6
Refactor dispatch signature using predefined types
#46
pagpires
closed
2 years ago
2
[DOC] Correct inaccuracy in SeqLike documentation
#45
ericmjl
closed
2 years ago
2
Pin mkdocs-material to 8.1.3
#44
ericmjl
closed
2 years ago
1
docs: add sugatoray as a contributor for infra, maintenance
#43
allcontributors[bot]
closed
2 years ago
0
Dispatch based on SeqLikeType.__args__
#42
ericmjl
closed
2 years ago
3
[BUG] `seq_type` handling during instantiation
#41
pagpires
closed
2 years ago
5
docs: add pagpires as a contributor for doc
#40
allcontributors[bot]
closed
2 years ago
0
Consider using version pins for mkdocs-material to avoid code-breaking
#39
sugatoray
closed
2 years ago
2
omit #noqa in docoumentation
#38
pagpires
closed
2 years ago
1
noqa in documentation
#37
pagpires
closed
2 years ago
5
Add source code pro font to the distributed package
#36
andrewgiessel
closed
2 years ago
2
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