[Biopython] Getting ABI peak values from ABI file

[Eric Ma]

Thanks Peter! My pleasure to give back in little ways.

On Fri, Oct 7, 2016 at 1:21 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Hi Eric,
>
> About the numbering, I don't know - it is surely in the documentation
> somewhere, but you can probably work it out by comparing the graph
> you've made (or a tool like Chromas) against the called sequence.
>
> Thanks for looking into writing this example up for our website :)
>
> Peter
>
> On Fri, Oct 7, 2016 at 6:15 PM, Eric Ma <ericmajinglong at gmail.com> wrote:
> > 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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