[Biopython] .ab1 file parser in biopython?

[Uri Laserson]

I also found the following code lying around somewhere.  I copied it into
one of my repositories:

https://github.com/laserson/pytools/blob/master/ab1.py

"Python implementation of an ABIF file reader according to Applied
Biosystems' specificatons" as specified in March 2007, it appears.

...................................................................................
Uri Laserson
Graduate Student, Biomedical Engineering
Harvard-MIT Division of Health Sciences and Technology
M +1 917 742 8019
laserson at mit.edu


On Thu, Mar 10, 2011 at 04:00, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Mar 9, 2011 at 10:57 PM, Arvind Subramaniam
> <rasi at seas.harvard.edu> wrote:
> > Hi
> >  I am new to biopython so please excuse me if this issue is obviously
> > simple. I am trying to parse .ab1 sequencing trace files in Biopython
> > and I cannot find the right module or method to do this job. Can
> > someone suggest how I can parse .ab1 files?
> > Thanks,
> > Arvind.
>
> You mean the ABI trace file format for capillary sequencing?
>
> Personally I use EMBOSS seqret (e.g. to make FASTQ), or tracetuner
> if I want to recall the bases (the ABI software doesn't always to the
> best possible calling job).
>
> http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/seqret.html
> http://sourceforge.net/projects/tracetuner/
>
> Peter
>
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