Re: Sanger sequencing trace files support

Hi Jonas,

Are you happy to share sample file(s) using IUPAC ambiguity
codes like M = A or C which could be freely used by BioJava
and other projects as a test case?

(I'm specifically asking for Biopython as I'm not sure if anyone
has tried this with our ABI parser)

Thanks,

Peter

On Tue, Jul 12, 2016 at 4:26 PM, 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.
>
> Thank you for this useful API,
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