<div dir="ltr">Thank you, Peter! It worked like a charm, managed to get all 4 channels out.<div><br></div><div>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.<br><br><div class="gmail_quote"><div dir="ltr">On Fri, Oct 7, 2016 at 11:11 AM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Eric,<br class="gmail_msg">
<br class="gmail_msg">
I think you want the raw DATA1, DATA2, DATA3 and DATA4 values (for the<br class="gmail_msg">
four bases) which are exposed via the Biopython ABI parser, e.g.<br class="gmail_msg">
<br class="gmail_msg">
from Bio import SeqIO<br class="gmail_msg">
record = SeqIO.read("310.ab1", "abi")<br class="gmail_msg">
print(record.annotations['abif_raw']['DATA1'])<br class="gmail_msg">
<br class="gmail_msg">
See also <a href="http://www.appliedbiosystem.com/support/software_community/ABIF_File_Format.pdf" rel="noreferrer" class="gmail_msg" target="_blank">http://www.appliedbiosystem.com/support/software_community/ABIF_File_Format.pdf</a><br class="gmail_msg">
<br class="gmail_msg">
Peter<br class="gmail_msg">
<br class="gmail_msg">
On Fri, Oct 7, 2016 at 3:06 PM, Eric Ma <<a href="mailto:ericmajinglong@gmail.com" class="gmail_msg" target="_blank">ericmajinglong@gmail.com</a>> wrote:<br class="gmail_msg">
> I'd like to view the ABI peak values that are used for drawing<br class="gmail_msg">
> chromatograms, but I'm not quite sure how to do this using the BioPython<br class="gmail_msg">
> API. I've searched on the AbiIO documentation, and peeked at the source<br class="gmail_msg">
> code, but still could not see how to do this. Is it possible?<br class="gmail_msg">
><br class="gmail_msg">
> I've already tried hunting around on the internet, but the closest I could<br class="gmail_msg">
> find for an answer was:<br class="gmail_msg">
> <a href="http://biology.stackexchange.com/questions/35852/view-abi-chromatogram-plots-with-python" rel="noreferrer" class="gmail_msg" target="_blank">http://biology.stackexchange.com/questions/35852/view-abi-chromatogram-plots-with-python</a>,<br class="gmail_msg">
> in which Peter mentioned that the chromatogram data should be exposed in<br class="gmail_msg">
> 1.66.<br class="gmail_msg">
><br class="gmail_msg">
> _______________________________________________<br class="gmail_msg">
> Biopython mailing list  -  <a href="mailto:Biopython@mailman.open-bio.org" class="gmail_msg" target="_blank">Biopython@mailman.open-bio.org</a><br class="gmail_msg">
> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython" rel="noreferrer" class="gmail_msg" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br class="gmail_msg">
</blockquote></div></div></div>