Re: Sanger sequencing trace files support

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On Tue, Jul 12, 2016 at 10:26 AM, Jonas Dehairs <[email protected]>
wrote:

> The 4.2 API currently does not have methods for importing and
> handeling Sanger sequencing files (ABI, SCF). I'm currently resorting
> to the legacy classes in 1.9.1 (ChromatogramFactory and Chromatogram).
>
> ChromatogramFactory only supports Sanger trace files with standard
> ATGCN characters. It throws a
> UnsupportedChromatogramFormatException upon reading Sanger files with
> IUPAC Ambiguity Codes (for example M = A or C). Even if I would just
> like to access the traces and ignore the base calls, this is
> impossible with the current implementation since we can't even open
> the file if it contains Ambiguity codes.
>
> On a side note, I have been getting more and more questions from users
> why they can't open their Sanger sequencing files (in my program that
> uses BioJava). I think the popularity of CRISPR and the
> characterization of CRISPR KO clones (which is likely to result in
> heterozygous base calls) is increasing the number of people that have
> these IUPAC Ambiguity Sanger files.
>
> For now, I tell people to go back to the Sanger sequencing software
> that exports the ABI or SCF files and disable IUPAC Ambiguity in the
> export options. In that case the base calling algorithm just picks the
> strongest signals in case of ambiguity and sticks to standard ATGCN
> characters.
>
> Anyway, I am requesting the addition of the Chromatogram classes to
> the new API with support for opening files if they contain UPAC
> Ambiguity Codes.
>

The biojava 1.9.x codebase is still maintained at

https://github.com/biojava/biojava-legacy

If you created a pull request to add IUPAC Ambiguity Codes support to
ChromatogramFactory, a 1.9.3 release is planned for later this summer, and
it could go in then.

   michael

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<div dir=3D"ltr">On Tue, Jul 12, 2016 at 10:26 AM, Jonas Dehairs <span dir=
=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=3D"_blank">j=
[email protected]</a>&gt;</span> wrote:<br><div class=3D"gmail_extra">=
<div class=3D"gmail_quote"><blockquote class=3D"gmail_quote" style=3D"margi=
n:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex=
">The 4.2 API currently does not have methods for importing and<br>
handeling Sanger sequencing files (ABI, SCF). I&#39;m currently resorting<b=
r>
to the legacy classes in 1.9.1 (ChromatogramFactory and Chromatogram).<br>
<br>
ChromatogramFactory only supports Sanger trace files with standard<br>
ATGCN characters. It throws a<br>
UnsupportedChromatogramFormatException upon reading Sanger files with<br>
IUPAC Ambiguity Codes (for example M =3D A or C). Even if I would just<br>
like to access the traces and ignore the base calls, this is<br>
impossible with the current implementation since we can&#39;t even open<br>
the file if it contains Ambiguity codes.<br>
<br>
On a side note, I have been getting more and more questions from users<br>
why they can&#39;t open their Sanger sequencing files (in my program that<b=
r>
uses BioJava). I think the popularity of CRISPR and the<br>
characterization of CRISPR KO clones (which is likely to result in<br>
heterozygous base calls) is increasing the number of people that have<br>
these IUPAC Ambiguity Sanger files.<br>
<br>
For now, I tell people to go back to the Sanger sequencing software<br>
that exports the ABI or SCF files and disable IUPAC Ambiguity in the<br>
export options. In that case the base calling algorithm just picks the<br>
strongest signals in case of ambiguity and sticks to standard ATGCN<br>
characters.<br>
<br>
Anyway, I am requesting the addition of the Chromatogram classes to<br>
the new API with support for opening files if they contain UPAC<br>
Ambiguity Codes.<br></blockquote><div><br></div><div>The biojava 1.9.x code=
base is still maintained at<br><br><a href=3D"https://github.com/biojava/bi=
ojava-legacy">https://github.com/biojava/biojava-legacy<br></a><br></div><d=
iv>If you created a pull request to add IUPAC Ambiguity Codes support to Ch=
romatogramFactory, a 1.9.3 release is planned for later this summer, and it=
 could go in then.<br><br></div><div>=C2=A0=C2=A0 michael<br></div></div></=
div></div>

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