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

[Peter]

On Tue, Sep 15, 2009 at 4:02 PM, natassa <natassa_g_2000 at yahoo.com> wrote:
>
>> If you prefer to work in Python, it should be easy to recreate
>> a Biopython version of the same script. Which script are we
>> talking about? Is it publicly available?
>
> It is called shuffleSequences_fasta.pl and goes along with the
> (free) distribution of velvet (Zerbino, EBI). The script is really
> simple.

Oh right - you can see the scripts on Daniel's github repository,
http://github.com/dzerbino/velvet

Both scripts are very very simple minded, which means fixing
the bug will actually be a big change:

shuffleSequences_fasta.pl appears to assume every FASTA
entry is exactly two lines (a safe assumption for short reads
like 36bp from early Solexa/Illumina), but not a safe choice
in general as wrapping in FASTA is normal.

shuffleSequences_fastq.pl appears to assume every FASTQ
entry is exactly four lines (a reasonable assumption, especially
for short reads like 36bp reads from early Solexa/Illumina),
but not a safe choice in general as FASTQ files can also be
wrapped (even if it is discouraged).

We should be able to mimic these in Biopython using SeqIO...

Peter