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.