[Biopython] SeqIO for fasta conversion of Illumina files with > 60 bp

[Peter]

On Tue, Sep 15, 2009 at 5:43 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> Rather than using itertools, you could also write a simple generator
> function to do the pairing explicitly. Assuming you are dealing with
> paired end reads, it would make sense to explicitly check the IDs
> match up as expected.

I confess I didn't actually test that example (I don't have Python 2.6
on this machine), and I had miss read the itertools.izip_longest
documentation - that won't actually work as is. Sorry :(

Instead, here is a simple interleaving using a generator function,
which I *have* tested on Python 2.5,

from Bio import SeqIO
#Setup variables (could parse command line args here)
fileA = "SRR001666_1.fastq"
fileB = "SRR001666_2.fastq
fileOut = "SRR001666_interleaved.fastq"
format = "fastq"
#Setup the input
def interleave(iter1, iter2) :
    while True :
        yield iter1.next()
        yield iter2.next()
recordsA = SeqIO.parse(open(fileA,"rU"), format)
recordsB = SeqIO.parse(open(fileB,"rU"), format)
records = interleave(recordsA, recordsB)
#Now the output
handle = open(fileOut, "w")
count = SeqIO.write(records, handle, format)
handle.close()
print "%i records written to %s" % (count, fileOut)

Note that this does not check the number of records in the two
files matches, nor does it do any explicit test on the record ids.

Peter