[Biojava-l] ab1 files

[Trent Schafer]

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