[Biopython] Getting ABI peak values from ABI file

[Peter Cock]

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.
>> >> >
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