Seqlike
Unified biological sequence manipulation in Python
Install / Use
/learn @modernatx/SeqlikeREADME
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<h1 align="center"> SeqLike - flexible biological sequence objects in Python </h1>
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Introduction
A single object API that makes working with biological sequences in Python more ergonomic. It'll handle anything like a sequence.
Built around the Biopython SeqRecord class, SeqLikes abstract over the semantics of molecular biology (DNA -> RNA -> AA) and data structures (strings, Seqs, SeqRecords, numerical encodings) to allow manipulation of a biological sequence at the level which is most computationally convenient.
Code samples and examples
Build data-type agnostic functions
def f(seq: SeqLikeType, *args):
seq = SeqLike(seq, seq_type="nt").to_seqrecord()
# ...
Streamline conversion to/from ML friendly representations
prediction = model(aaSeqLike('MSKGEELFTG').to_onehot())
new_seq = ntSeqLike(generative_model.sample(), alphabet="-ACGTUN")
Interconvert between AA and NT forms of a sequence
Back-translation is conveniently built-in!
s_nt = ntSeqLike("ATGTCTAAAGGTGAA")
s_nt[0:3] # ATG
s_nt.aa()[0:3] # MSK, nt->aa is well defined
s_nt.aa()[0:3].nt() # ATGTCTAAA, works because SeqLike now has both reps
s_nt[:-1].aa() # TypeError, len(s_nt) not a multiple of 3
s_aa = aaSeqLike("MSKGE")
s_aa.nt() # AttributeError, aa->nt is undefined w/o codon map
s_aa = aaSeqLike(s_aa, codon_map=random_codon_map)
s_aa.nt() # now works, backtranslated to e.g. ATGTCTAAAGGTGAA
s_aa[:1].nt() # ATG, codon_map is maintained
Easily plot multiple sequence alignments
seqs = [s for s in SeqIO.parse("file.fasta", "fasta")]
df = pd.DataFrame(
{
"names": [s.name for s in seqs],
"seqs": [aaSeqLike(s) for s in seqs],
}
)
df["aligned"] = df["seqs"].seq.align()
df["aligned"].seq.plot()
Flexibly build and parse numerical sequence representations
# Assume you have a dataframe with a column of 10 SeqLikes of length 90
df["seqs"].seq.to_onehot().shape # (10, 90, 23), padded if needed
To see more in action, please check out the docs!
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Install the library with pip or conda.
With pip
pip install seqlike
With conda
conda install -c conda-forge seqlike
Authors
Support
- Questions about usage should be posed on Stack Overflow with the #seqlike tag.
- Bug reports and feature requests are managed using the Github issue tracker.
Contributors ✨
Thanks goes to these wonderful people (emoji key):
<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --> <!-- prettier-ignore-start --> <!-- markdownlint-disable --> <table> <tbody> <tr> <td align="center"><a href="https://github.com/ndousis"><img src="https://avatars.githubusercontent.com/u/15198691?v=4?s=100" width="100px;" alt="Nasos Dousis"/><br /><sub><b>Nasos Dousis</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=ndousis" title="Code">💻</a></td> <td align="center"><a href="http://giessel.com"><img src="https://avatars.githubusercontent.com/u/1160997?v=4?s=100" width="100px;" alt="andrew giessel"/><br /><sub><b>andrew giessel</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=andrewgiessel" title="Code">💻</a></td> <td align="center"><a href="https://github.com/maxasauruswall"><img src="https://avatars.githubusercontent.com/u/14082213?v=4?s=100" width="100px;" alt="Max Wall"/><br /><sub><b>Max Wall</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=maxasauruswall" title="Code">💻</a> <a href="https://github.com/modernatx/seqlike/commits?author=maxasauruswall" title="Documentation">📖</a></td> <td align="center"><a href="https://ericmjl.github.io/"><img src="https://avatars.githubusercontent.com/u/2631566?v=4?s=100" width="100px;" alt="Eric Ma"/><br /><sub><b>Eric Ma</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=ericmjl" title="Code">💻</a> <a href="https://github.com/modernatx/seqlike/commits?author=ericmjl" title="Documentation">📖</a></td> <td align="center"><a href="https://github.com/MihirMetkar"><img src="https://avatars.githubusercontent.com/u/9938754?v=4?s=100" width="100px;" alt="Mihir Metkar"/><br /><sub><b>Mihir Metkar</b></sub></a><br /><a href="#ideas-MihirMetkar" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/modernatx/seqlike/commits?author=MihirMetkar" title="Code">💻</a></td> <td align="center"><a href="https://github.com/mccaron707"><img src="https://avatars.githubusercontent.com/u/26267127?v=4?s=100" width="100px;" alt="Marcus Caron"/><br /><sub><b>Marcus Caron</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=mccaron707" title="Documentation">📖</a></td> <td align="center"><a href="https://github.com/pagpires"><img src="https://avatars.githubusercontent.com/u/7856031?v=4?s=100" width="100px;" alt="pagpires"/><br /><sub><b>pagpires</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=pagpires" title="Documentation">📖</a></td> </tr> <tr> <td align="center"><a href="https://www.linkedin.com/in/sugatoray/"><img src="https://avatars.githubusercontent.com/u/10201242?v=4?s=100" width="100px;" alt="Sugato Ray"/><br /><sub><b>Sugato Ray</b></sub></a><br /><a href="#infra-sugatoray" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-sugatoray" title="Maintenance">🚧</a></td> <td align="center"><a href="http://dmnfarrell.github.io/"><img src="https://avatars.githubusercontent.com/u/7859189?v=4?s=100" width="100px;" alt="Damien Farrell"/><br /><sub><b>Damien Farrell</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=dmnfarrell" title="Code">💻</a></td> <td align="center"><a href="https://github.com/farbod-nobar"><img src="https://avatars.githubusercontent.com/u/44842525?v=4?s=100" width="100px;" alt="Farbod Mahmoudinobar"/><br /><sub><b>Farbod Mahmoudinobar</b></sub></a><br /><a href="https://github.com/modernatx/seqlike/commits?author=farbod-nobar" title="Code">💻</a></td> <td align="center"><a href="https://github.com/JacobHayes"><img src="https://avatars.githubusercontent.com/u/2555532?v=4?s=100" width="100px;" alt="Jacob Hayes"/><br /><sub><b>Jacob Hayes</b></sub></a><br /><a href="#infra-JacobHayes" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td> </tr> </tbody> </table> <!-- markdownlint-restore --> <!-- prettier-ignore-end --> <!-- ALL-CONTRIBUTORS-LIST:END -->This project follows the all-contributors specification. Contributions of any kind welcome!
