[Biopython] Getting ABI peak values from ABI file

[Eric Ma]

Thank you, Peter! It worked like a charm, managed to get all 4 channels out.

I also read the documentation a bit further: DATA9-DATA12 contain the
values that are conventionally displayed. I was able to use that to make a
simple matplotlib line plot on my own.

On Fri, Oct 7, 2016 at 11:11 AM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hi Eric,
>
> I think you want the raw DATA1, DATA2, DATA3 and DATA4 values (for the
> four bases) which are exposed via the Biopython ABI parser, e.g.
>
> from Bio import SeqIO
> record = SeqIO.read("310.ab1", "abi")
> print(record.annotations['abif_raw']['DATA1'])
>
> See also
> http://www.appliedbiosystem.com/support/software_community/ABIF_File_Format.pdf
>
> Peter
>
> On Fri, Oct 7, 2016 at 3:06 PM, Eric Ma <ericmajinglong at gmail.com> wrote:
> > I'd like to view the ABI peak values that are used for drawing
> > chromatograms, but I'm not quite sure how to do this using the BioPython
> > API. I've searched on the AbiIO documentation, and peeked at the source
> > code, but still could not see how to do this. Is it possible?
> >
> > I've already tried hunting around on the internet, but the closest I
> could
> > find for an answer was:
> >
> http://biology.stackexchange.com/questions/35852/view-abi-chromatogram-plots-with-python
> ,
> > in which Peter mentioned that the chromatogram data should be exposed in
> > 1.66.
> >
> > _______________________________________________
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> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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