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Project description

quickdna

quickdna is a simple, fast library for working with DNA sequences.

>>> from quickdna import DnaSequence, ProteinSequence
>>> d = DnaSequence("taatcaagactattcaaccaa")
>>> d.translate()
ProteinSequence(seq='*SRLFNQ')
>>> d.translate(table=22)
ProteinSequence(seq='**RLFNQ')
>>> d.translate_all_frames()
(ProteinSequence(seq='*SRLFNQ'), ProteinSequence(seq='NQDYST'), ProteinSequence(seq='IKTIQP'))
>>> d[3:9].translate()
ProteinSequence(seq='SR')
>>> d[3:9].reverse_complement()
DnaSequence(seq='TCTTGA')

quickdna is much faster than Biopython for regular DNA translation tasks.

task	time	comparison
translate_quickdna(small_genome)	0.00306ms / iter
translate_biopython(small_genome)	0.05834ms / iter	1908.90%
translate_quickdna(covid_genome)	0.02959ms / iter
translate_biopython(covid_genome)	3.54413ms / iter	11979.10%
reverse_complement_quickdna(small_genome)	0.00238ms / iter
reverse_complement_biopython(small_genome)	0.00398ms / iter	167.24%
reverse_complement_quickdna(covid_genome)	0.02409ms / iter
reverse_complement_biopython(covid_genome)	0.02928ms / iter	121.55%

Project details

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0.5.0

Jan 9, 2023

0.2.0

Jan 14, 2022

0.1.3

Jan 13, 2022

0.1.2

Jan 13, 2022

This version

0.1.1

Jan 12, 2022

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