<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">You are welcome to use the </span><span style="font-family:arial,sans-serif;font-size:13px">A6_1-DB3.ab1 test file. It is from a sequencing test on Amplicon 6 (A6_1) of the daf-2 gene in C. elegans to confirm a homozygous mutation after backcrossing the strain. DB3 stands for David Bulger's third primer, which was the primer used for sequencing. </span><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">However, the main reason I wanted to have access to the raw trace file data was for evaluation of heterozygous mutations, since Phred2 quality scores and the default bases called cannot be used for this purpose. Thus, it might be better to use a file with a heterozygous mutation (gk169915) as a test file (attached).<div>
<font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">2_5-DB29.ab1</font></div><div><font face="arial, sans-serif">Amplicon 2 (2_5) of daf-2 C. elegans gene using David Bulger's Primer 29 (DB29)<br>
</font><div><br></div><div>Many thanks to Mike for your help getting this problem with the Biopython AbiIO out into the open. Peter and Bow, many thanks for taking the time to look into this problem and come up with a creative solution. The new dictionary in SeqRecord sounds like a much more flexible option than the simple additions of 'extra tags' for DATA9-DATA12 and PLOC1.</div>
<div><br></div><div>All the Best,</div><div>David</div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jul 10, 2014 at 11:25 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Great - I've checked in the initial work to the main branch,<br>
<a href="https://github.com/biopython/biopython/commit/b20f3641a5eaae5df1d25de5ece8b7d8db441e3e" target="_blank">https://github.com/biopython/biopython/commit/b20f3641a5eaae5df1d25de5ece8b7d8db441e3e</a><br>
<br>
Peter<br>
<div class=""><br>
On Thu, Jul 10, 2014 at 9:40 AM, Mike Cariaso <<a href="mailto:cariaso@gmail.com">cariaso@gmail.com</a>> wrote:<br>
> no thanks are necessary (quite the reverse), but they are welcomed.<br>
><br>
><br>
> On Thu, Jul 10, 2014 at 9:25 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br>
> wrote:<br>
>><br>
>> Hello from the pre-BOSC Codefest, where Bow and I have been<br>
>> looking at the Bio.SeqIO ABI parser in response to an email from<br>
>> Mike & David (CC'd, see below).<br>
>><br>
>> All the different versions of the ABI capillary sequencers record<br>
>> additional tags to the binary file which would record all sorts of<br>
>> extra information like voltages and the raw colour data.<br>
>><br>
>> Mike & David wanted access to some of this data, but the SeqIO<br>
>> parser was not exposing it. Our proposal is to add a new dictionary<br>
>> to the SeqRecord's annotations containing all the raw data so that<br>
>> advanced users can do further processing.<br>
>><br>
>> I'm going to work on this code today, adding a few more tests etc.<br>
>><br>
>> Mike & David - are you happy to be thanked by name in the<br>
>> commit comment (e.g. "With input from ...")?<br>
>><br>
>> Mike - I am intending to incorporate your test file A6_1-DB3.ab1<br>
>> into the Biopython unit test collection.<br>
>><br>
>> Thanks,<br>
>><br>
>> Peter<br>
>><br>
>> ---------- Forwarded message ----------<br>
</div>>> <snip><br>
</blockquote></div><br></div>