PyCogent 3: Translation

I'm continuing with an exploration of PyCogent (first post here). I found a draft cookbook on the web. That will be a big help!

The problem that I had in following the first tutorial is this: the function LoadSeqs creates an object of this class:

<class 'cogent.core.alignment.SequenceCollection'>

What we want is a single DNA sequence. We can get the individual sequences back from the collection like so:

from cogent import LoadSeqs, DNA fn = 'SThemA.fasta' s = LoadSeqs(fn,moltype=DNA,aligned=False) name,seq = s.items()[0]

seq is now a

<class 'cogent.core.sequence.DnaSequence'>

and it supports slicing. We can also construct a similar object directly:

seq2 = DNA.makeSequence("AGTACACTGGT") seq2.Name = 'X' print seq2.toFasta()

>X AGTACACTGGT

We still can't translate a stop codon:

pep = seq.getTranslation()

cogent.core.alphabet.AlphabetError: TAG

But slicing makes it easy to fix that:

pep = seq[:-3].getTranslation() print type(pep) print pep[:24]

<class 'cogent.core.sequence.ProteinSequence'> MTLLALGINHKTAPVSLRERVTFS

Sequences are complex objects:

L = dir(seq) L = [e for e in L if not e[0] == '_'] for e in L[:10]: print e print len(L), 'items'

CodonAlphabet Info LineWrap MW MolType Name PROTEIN addAnnotation addFeature annotateFromGff 81 items

Going through the dir reveals the intended method for translating with a terminal stop:

seq = DNA.makeSequence("ATGACACTGGTGTAG") seq.Name = 'X' print seq.toFasta() print seq.hasTerminalStop() seq2 = seq.withoutTerminalStopCodon() print seq2.getTranslation() # reverse complement print seq.rc().canPair(seq)

>X ATGACACTGGTGTAG True MTLV True