Adding an example of usage of SeqIO.

source/_static/code/seq_io.py

+#!/usr/bin/env python3
+"""Example of use of SeqIO from biopython
+
+Here, we parse a fasta file, put the records in a list, search for a motif in
+the sequence of the first record, and create a subsequence around this motif.
+"""
+
+from Bio import SeqIO
+
+records = list(SeqIO.parse(fasta_filename, "fasta"))
+records
+# [SeqRecord(seq=Seq('GCCTCGGCCTCTGCATAAATAAAAAAAATTAGTCAGCCATGGGGCGGAGAATGG...GCG', SingleLetterAlphabet()), id='gi|965480|gb|J02400.1|SV4CG', name='gi|965480|gb|J02400.1|SV4CG', description='gi|965480|gb|J02400.1|SV4CG Simian virus 40 complete genome', dbxrefs=[])]
+sequence = records[0].seq
+sequence
+# Seq('GCCTCGGCCTCTGCATAAATAAAAAAAATTAGTCAGCCATGGGGCGGAGAATGG...GCG', SingleLetterAlphabet())
+motif = "TAAAT"
+sequence.find(motif)
+# 15
+motif_pos = sequence.find(motif)
+subseq_start = motif_pos - 10
+subseq_end = motif_pos + len(motif) + 11
+subseq = sequence[subseq_start:subseq_end]
+subseq
+# Seq('GGCCTCTGCATAAATAAAAAAAATTA', SingleLetterAlphabet())
+