• Cookbook

Converting sequence files with the Bio.SeqIO module.

Problem

Many bioinformatics tools take different input file formats, so there is a common need to interconvert between sequence file formats. One useful option is the commandline tool seqret from EMBOSS, but here we’ll show how to tackle this problem with Bio.SeqIO.

Solution

Suppose you have a GenBank file which you want to turn into a Fasta file. For example, let’s consider the file cor6_6.gb (which is included in the Biopython unit tests under the GenBank directory):

from Bio import SeqIO

with open("cor6_6.gb", "rU") as input_handle:
    with open("cor6_6.fasta", "w") as output_handle:
        sequences = SeqIO.parse(input_handle, "genbank")
        count = SeqIO.write(sequences, output_handle, "fasta")

print("Converted %i records" % count)

In this example the GenBank file contained six records and started like this:

LOCUS       ATCOR66M      513 bp    mRNA            PLN       02-MAR-1992
DEFINITION  A.thaliana cor6.6 mRNA.
ACCESSION   X55053
VERSION     X55053.1  GI:16229
...

The resulting Fasta file also contains all six records and looks like this:

>X55053.1 A.thaliana cor6.6 mRNA.
AACAAAACACACATCAAAAACGATTTTACAAGAAAAAAATA...
...

Note that all the Fasta file can store is the identifier, description and sequence.

By changing the format strings, that code could be used to convert between any supported file formats.

You don’t have to work with file handles - see this example using stdin and stdout pipes with Bio.SeqIO.

How it works

See the Bio.SeqIO page.