Bioinformatics with Python Cookbook - Second Edition

How to do it...

Let's take a look at the following steps:

1. As our sequence of interest is available in a Biopython sequence object, let's start by saving it to a FASTA file on our local disk:

from Bio import SeqIOw_hdl = open('example.fasta', 'w')w_seq = seq[11:5795]SeqIO.write([w_seq], w_hdl, 'fasta')w_hdl.close()

The SeqIO.write function takes a list of sequences to write (not just a single one). Be careful with this idiom. If you want to write many sequences (and you could easily write millions with NGS), do not use a list (as shown in the preceding code), because this will allocate massive amounts of memory. Either use an iterator, or use the SeqIO.write function several times with a subset of the sequence on each write.

2. In most situations, ...