[Biojava-l] ab1 files

[Amr AL-Hossary]

If we agreed on migrating the code to Biojava3, I can do it.
especially as I haven't done something useful on the group for a while.

Amr

--------------------------------------------------
From: "Scooter Willis" <HWillis at scripps.edu>
Sent: Friday, July 29, 2011 3:11 AM
To: "Trent Schafer" <tr3nton at gmail.com>; "Biojava-l at lists.open-bio.org" 
<biojava-l at lists.open-bio.org>
Subject: Re: [Biojava-l] ab1 files

> Trent
>
> We do not have support for AB1 files in Biojava3. Do you have any interest
> in working/migrating the code for the AB1 file parser? I can assist if you
> want to work on it.
>
> Scooter
>
> On 7/28/11 7:32 PM, "Trent Schafer" <tr3nton at gmail.com> wrote:
>
>>Hi,
>>
>>Not sure if anyone can help or advise - still just trying to figure it
>>out.
>>
>>We are using this database software to manage our clinical studies, and we
>>want to add the functionality to store sequencing files, and hopefully
>>some
>>useful information extracted from the files we upload.
>>
>>I found in the legacy cookbooks the following:
>>http://biojava.org/wiki/BioJava:Cookbook:SeqIO:ABItoSequence and based on
>>an
>>AB1 file I have on my workstation, was able to successfully run the code
>>listed - I presume its also possible to extract the quality scores?
>>
>>Anyway, was trying to see if these files can be read in BioJava 3.x?
>>
>>I was trying the 2 examples listed here:
>>http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite but the
>>exception is thrown: Exception in thread "main"
>>org.biojava3.core.exceptions.CompoundNotFoundError: Compound not found
>>for:
>>Cannot find compound for:
>>
>>So my assumption is that it just doesn't know how to read AB1 files?
>>
>>To summarise, is it only possible read AB1 files in the legacy version of
>>the software? I assume its better to be using 3.x if possible? There is a
>>section of the 3.x cookbook:
>>http://biojava.org/wiki/BioJava:CookBook:Core:Sequences is it that this
>>hasn't been implemented yet, or is just undocumented?
>>
>>Any information is much appreciated.
>>
>>Thx,
>>Trent
>>_______________________________________________
>>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>