[Biopython] Getting ABI peak values from ABI file

[Eric Ma]

Working on a contribution right now!
https://github.com/ericmjl/biopython.github.io

By the way, I was wondering if it's possible to know what letter each data
channel corresponds to? It isn't clear from the ABI documentation whether
it is 9-A, 10-T, 11-G, 12-C or something else.

On Fri, Oct 7, 2016 at 12:36 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Great - glad to know that worked as expected.
>
> If you would like to share the script, that would be great?
>
> It might fit nicely under the website cookbook section,
> http://biopython.org/wiki/Category:Cookbook - this used
> to be a wiki which was probably easier to add to, but it
> is now on GitHub.
>
> Thanks,
>
> Peter
>
> On Fri, Oct 7, 2016 at 5:22 PM, Eric Ma <ericmajinglong at gmail.com> wrote:
> > 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.
> >> >
> >> > _______________________________________________
> >> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> >> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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