Overview

From String

A sequence can be made from a string using:

>>> import valerius
>>> sequence1 = valerius.from_string("MALWMRLLPL")
>>> sequence2 = valerius.from_string("ggttgaactactcat")

valerius will automatically detect which sequence type it is, and will return a PeptideSequence for example, or RnaSequence as required.

Basic properties can be queried:

>>> "LLP" in sequence1
True
>>> sequence1.type
'peptide'
>>> sequence.length
10
>>> sequence2.frequencies
Counter({'T': 5, 'A': 4, 'G': 3, 'C': 3})
>>> sequence1.codes
['MET', 'ALA', 'LEU', 'TRP', 'MET', 'ARG', 'LEU', 'LEU', 'PRO', 'LEU']
>>> sequence2.gc_content
0.4

Opening

You can open a file…

>>> sequence = valerius.open("my_sequence.fasta")
>>> sequence
<DnaSequence (length: 163)>

…or fetch them…

>>> sequence = valerius.fetch("P01308")
<PeptideSequence (length: 110)>