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" <[email protected]> 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 - [email protected] >http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
