(:source lang=python:)

""" Database file parsing in biopython - Fasta - GenBank - SwissProt see section 5.1 in the biopython tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html The SeqRecord class is described in section 4.1 """

from Bio import SeqIO parser = SeqIO.parse("cam.fasta", "fasta") print parser record = parser.next()

1. it is an iterator we can loop thru FastaIterator using a for loop:

from Bio import SeqIO for seq_record in SeqIO.parse("cam.fasta", "fasta") :

    print seq_record.id 
    print seq_record.seq 
    print len(seq_record.seq) 

1. Essentially the same code can be used to go thru files in uniprot format

from Bio import SeqIO parser = SeqIO.parse("cam.txt", "swiss") print parser record = parser.next()

from Bio import SeqIO for seq_record in SeqIO.parse("cam.txt", "swiss") :

    print seq_record.id 
    print seq_record.seq 
    print len(seq_record.seq) 

1. If we had a file in genbank format we give the string "genbank" as
2. an argument to the parse function.

from Bio import SeqIO for seq_record in SeqIO.parse("cam.gbk", "genbank") :

    print seq_record.id 
    print seq_record.seq 
    print len(seq_record.seq) 

1. Note: use the 'read' function in SeqIO to read data from a sequence file that
2. contains a single record.
3. getting a list of records:

from Bio import SeqIO

1. using list comprehensions

records = [record for record in SeqIO.parse("cam.fasta", "fasta")]

1. or using the list constructor:

records = list(SeqIO.parse("cam.fasta", "fasta"))

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