[Biopython] Getting ABI peak values from ABI file

[Peter Cock]

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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