Hello. Whilst BioJava supports the < and > annotation, and will correctly load these from the file and store them as FuzzyLocations internally, when it is asked to write them to BioSQL they are lost. This is BioSQL has no way of storing this information. Therefore when you save the sequence into BioSQL and load it back in later, the < and > are lost.
cheers, Richard Bandaru, Sandya (NIH/NIAID) [C] wrote: > Hi, > > I used BioJava 1.6 to store Genbank sequences into MySQL database, and tried > writing out the Sequence. I noticed the feature location is not having '<' or > '>' (if is partial gene/CDS). I looked into the documentation of biojavax and > didn't find way to get this information. > > I found FuzzyLocation in Biojava. I appreciate if you can provide similar > feature to get the partial CDS/gene locations. > > Thanks to the BioJava team for the good work. > > Regards, > Sandya Bandaru > Bioinformatics Software Developer > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > 10401 Fernwood Road > Bethesda, MD 20892 > > Disclaimer: The information in this e-mail and any of its attachments is > confidential and may contain sensitive information. It should not be used by > anyone who is not the original intended recipient. If you have received this > e-mail in error please inform the sender and delete it from your mailbox or > any other storage devices. National Institute of Allergy and Infectious > Diseases shall not accept liability for any statements made that are sender's > own and not expressly made on behalf of the NIAID by one of its > representatives > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l
