[Biopython] fastq-solexa index

[Peter]

On Thu, Nov 26, 2009 at 12:49 AM, xyz <mitlox at op.pl> wrote:
> Hello,
> On this page ( http://www.biopython.org/wiki/SeqIO ) I have found that
> biopython can use fastq-solexa index. What does it means and are there any
> examples?
>
> Thank you in advance.

In Bio.SeqIO we give each file format a name, in this case "fastq-solexa"
means the old Solexa FASTQ files (also used by Illumina up to and
including pipeline 1.2) which use Solexa scores with an ASCII offset
of 64 (not PHRED scores). The table on the SeqIO wiki page tries to
summarise this. See also: http://en.wikipedia.org/wiki/FASTQ_format

The "index" column on that table on the SeqIO wiki page indicates if
each file format can be used with the Bio.SeqIO.index(...) function
included in Biopython 1.52 onwards. See:
http://news.open-bio.org/news/2009/09/biopython-seqio-index/

There are also examples in the main Tutorial,
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

And in the Bio.SeqIO module's built in help, online here:
http://biopython.org/DIST/docs/api/Bio.SeqIO-module.html

>From within Python:

>>> from Bio import SeqIO
>>> help(SeqIO)
...
>>> help(SeqIO.index)
...

Peter