[Biojava-l] ab1 files

Scooter Willis HWillis at scripps.edu
Fri Jul 29 01:11:46 UTC 2011


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.


On 7/28/11 7:32 PM, "Trent Schafer" <tr3nton at gmail.com> wrote:

>Not sure if anyone can help or advise - still just trying to figure it
>We are using this database software to manage our clinical studies, and we
>want to add the functionality to store sequencing files, and hopefully
>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
>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
>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.
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