Protein sequences

Creating a ProteinSequence with a name

>>> from cogent import PROTEIN
>>> p = PROTEIN.makeSequence('THISISAPRQTEIN','myProtein')
>>> type(p)
<class 'cogent.core.sequence.ProteinSequence'>
>>> str(p)
'THISISAPRQTEIN'

Converting a DNA sequence string to protein sequence string

>>> from cogent.core.genetic_code import DEFAULT as standard_code
>>> standard_code.translate('TTTGCAAAC')
'FAN'

Conversion to a ProteinSequence from a DnaSequence is shown in Translate a DnaSequence to protein.

Loading protein sequences from a Phylip file

>>> from cogent import LoadSeqs, PROTEIN
>>> seq = LoadSeqs('data/abglobin_aa.phylip', moltype=PROTEIN,
...              aligned=True)

Loading other formats, or collections of sequences is shown in Loading nucleotide, protein sequences.