Re: ab1 files
"Amr AL-Hossary" <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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" <[email protected]> Sent: Friday, July 29, 2011 3:11 AM To: "Trent Schafer" <[email protected]>; "[email protected]" <[email protected]> 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" <[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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l