Skip to main content

No project description provided

Project description


SeqLike - flexible biological sequence objects in Python

PyPI - Supported Python Version PyPI - Package Version Conda - Platform Conda (channel only) Docs -


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": [ for s in seqs],
        "seqs": [aaSeqLike(s) for s in seqs],
df["aligned"] = df["seqs"].seq.align()

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!

Getting Started

Install the library with pip or conda.

With pip

pip install seqlike

With conda

conda install -c conda-forge seqlike



Contributors ✨

Thanks goes to these wonderful people (emoji key):

Nasos Dousis


andrew giessel


Max Wall

💻 📖

Eric Ma

💻 📖

Mihir Metkar

🤔 💻

Marcus Caron




Sugato Ray

🚇 🚧

Damien Farrell


This project follows the all-contributors specification. Contributions of any kind welcome!

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

seqlike-1.3.0.tar.gz (369.0 kB view hashes)

Uploaded source

Built Distribution

seqlike-1.3.0-py3-none-any.whl (371.7 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page