PyCogent 9: getting serious with Sequence

I'm exploring PyCogent (docs, download page)---first post here.

The most central and basic object type in PyCogent is Sequence. There are several ways to construct a DNA Sequence object. For the demo, I need to load a FASTA-formatted sequence, and recover the title and DNA sequence separately. (Substitute your own to follow along).

from cogent import LoadSeqs, DNA, Sequence def loadData(fn): FH = open(fn, 'r') data = FH.read() FH.close() return data fn = 'cogent/SThemA.fasta' data = loadData(fn) n,s = data.strip().split('\n',1) n = n[1:]

Now, here are five ways to create a DNA Sequence object:

# method 1: from a string seq = Sequence(moltype=DNA, name=n, seq=s) print '1', seq[:24] # method 2: from a text file tfn = 'cogent/SThemA.txt' seq = Sequence(moltype=DNA, filename=tfn, format='fasta') print '2', seq[:24] # method 3: from a file # guess format from extension seq = Sequence(moltype=DNA, filename=fn) print '3', seq[:24] # method 4: a method in DNA seq = DNA.makeSequence(s) seq.Name = n print '4', seq[:24] # method 5: by joining two DNA sequences a = DNA.makeSequence("AGTACACTGGT") seq2 = seq[:6] + a print '5', seq2 # method 6: from an NCBI record (via str) from cogent.db.ncbi import EFetch e = EFetch(db='nucleotide', rettype='fasta', id='154102') data = e.read() n,s = data.strip().split('\n',1) # go to method 1 seq = Sequence(moltype=DNA, name=n, seq=s) print '6', seq[:24]

output:

1 ATGACCCTTTTAGCGCTCGGTATT 2 ATGACCCTTTTAGCGCTCGGTATT 3 ATGACCCTTTTAGCGCTCGGTATT 4 ATGACCCTTTTAGCGCTCGGTATT 5 ATGACCAGTACACTGGT 6 ATGACCCTTTTAGCGCTCGGTATT

Here is one more that is a little trickier:

# method 7: using a parser from cogent.parse.fasta import FastaParser # must modify for lowercase f=open(fn) g = FastaParser(f) n,s = g.next() s = str(s).upper() # go to method 1 seq = Sequence(moltype=DNA, name=n, seq=s) print '7', seq[:24] # simpler use is uppercase sequence fn2 = '.temp' FH = open(fn2,'w') FH.write('>' + n + '\n' + s.upper()) FH.close() f=open(fn2) g = FastaParser(f) n,s = g.next() # go to method 1 seq = Sequence(moltype=DNA, name=n, seq=s) print '8', seq[:24]

7 ATGACCCTTTTAGCGCTCGGTATT 8 ATGACCCTTTTAGCGCTCGGTATT

We'll look at the most basic methods of DNA Sequence objects next.