[Biopython] 2 seqs in one Bio.SeqIO, is it possible?

Alan alanwilter at gmail.com
Tue Mar 17 15:44:20 UTC 2015


My ultimate scope is to generate a XML file with two sequences: one protein
sequence and one DNA sequence, like that:

…
<AAseq>XLLLAINGVTECFTFAAMS</AAseq>
<DNAseq>NTTCTCCTGCTTGCCATCAATGGAGTGACAGAGTGTTTCACATTTG</DNAseq>
…

But I am afraid that Bio.SeqIO can only keep one Seq object at a time per
record.

Hoping that I am wrong, can some tell me how to do it?

a0 is my target record:

SeqRecord(seq=Seq('XLLLAINGVTECFTFAAMS', ProteinAlphabet()),
id='sp|O07835|IORA_THEKO', name='sp|O07835|IORA_THEKO',
description='sp|O07835|IORA_THEKO Indolepyruvate oxidoreductase subunit
IorA OS=Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
GN=iorA PE=1 SV=2', dbxrefs=[])

and b0 is my source record, from which I only want the DNA sequence,
 b0.seq = Seq('NTTCTCCTGCTTGCCATCAATGGAGTGAC...TTG', DNAAlphabet())

Any help would be very much appreciated.

Many thanks in advance,

Alan

-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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