Basic functions for genomic sequence manipulation

Example use-cases

Create a sequence

import seq_toolkit

sequence = seq_toolkit.Seq()
sequence.simulate(n_bases=250, return_seq=True)

'GTTCAACTTTAACCAGCGGTTATGCTCTTCCATGTGAGTCGTAGTCGGGTTCGCACGAAAGAATTATTTATTGCTGCGATACGCAATGCATCTGGTTGTGGAGTTTCACCAGGCAGGCAATTAGTCCTATGCGGAACCTGCTGCTATAAAACGCATAAATTAACTGGCACACCAGGGAGGTAAGGGATGAGAGGCCTACAAGATTCCCATGTGCATATGGAGGGCGTACTGGATTCACGCGTTCGGAGGC'

Simulate a gene

import seq_toolkit

gene = seq_toolkit.Gene()
gene.create(n_exons=8, return_gene=False)
gene.plot()

• For more on ene simulation, see the following: example notebook

Manipulate a sequence

import seq_toolkit

seq = 'CGGGTTCGCACGAAAGAATTATTTATTGCTGCGATACGCAATGCATCTGGTTGTGGAGTTTCACCAGGCAGGCAATTAGTCCTATGCGGAACCTGCTGCTATAAAACGCAT'
sequence = seq_toolkit.SequenceManipulator(seq)

sequence.reverse_complement()

'ATGCGTTTTATAGCAGCAGGTTCCGCATAGGACTAATTGCCTGCCTGGTGAAACTCCACAACCAGATGCATTGCGTATCGCAGCAATAAATAATTCTTTCGTGCGAACCCG'

Installation

pip install seq-toolkit

To install the development version:

git clone https://github.com/mvinyard/seq-toolkit.git

cd ./seq-toolkit/; pip install -e .

Notes

For questions, please send an email to mvinyard@broadinstitute.org or open an issue.