[Biopython] Write operations for abi format in Bio.SeqIO

[Rohan Kanchana]

Hi Peter,

Thanks for your response. To address your earlier point about confusion in
writing ABI files from scratch, I suppose that BioPython could provide
default values for the fields users would not usually concern themselves
with (such as base order, mobility filenames, and lane number). These
values could then, of course, be overridden at the user's discretion.

Here are some use cases for writing/rewriting ABI files:

   - Modifying base calls on existing ABI files, like you previously
   mentioned
   - Modifying peak locations on existing ABI files (sometimes the
   automated base calling algorithm skips and/or double counts peaks in the
   sequencing trace)
   - Modifying traces of existing ABI files to remove noise and other
   sequencing artifacts
   - Generating new ABI files from scratch for the purposes of software
   testing
   - Converting data that is not in ABI format (such as data from an API)
   into ABI format, for storage or input into another software pipeline
   - Automated annotation of existing ABI files

In short, most of these use cases revolve around software pipelines or
libraries that accept ABI files as input. Oftentimes such software can't be
modified to allow alternative forms of input, so the ability to
generate/modify/preprocess ABI files would enable more technical users to
maximize the potential of such software. Some examples of software that
accept Sanger sequencing input include TIDE, ICE, and DECODR (full
disclosure – I worked on DECODR), as well as EditR.

Thanks,
Rohan

On Tue, Sep 28, 2021 at 9:46 AM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hello Rohan,
>
> The ABI format has a vast number of metadata fields which would make a
> writer rather complicated to use (except for the special case of
> loading an existing file, modifying it, and writing out the new
> version).
>
> Do you have a use case? The only one I can come up with it redoing the
> base calling, and then updating the called sequence in the ABI file.
>
> Thanks,
>
> Peter
>
> On Sun, Sep 26, 2021 at 8:34 PM Rohan Kanchana <rohankanchana at gmail.com>
> wrote:
> >
> > Dear all,
> >
> > I'm Rohan Kanchana, a student at MIT. I observed that Bio.SeqIO only
> supports read operations for the "abi" format. I have code that would
> support a write operation for the "abi" format, so I wanted to ask the
> following: why are write operations not currently supported by BioPython
> for the "abi" format? If there is no reason, would making such a
> contribution to the BioPython library be useful?
> >
> > Thanks,
> > Rohan
> > _______________________________________________
> > Biopython mailing list  -  Biopython at biopython.org
> > https://mailman.open-bio.org/mailman/listinfo/biopython
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20210928/5aae27b9/attachment.htm>