I generally don't recommend parsing the standard BLAST output as it keeps changing subtly . Best to parse one of the tabular formats or the XML output.
- Mark On Tue, Mar 16, 2010 at 11:19 PM, Andreas Prlic <[email protected]> wrote: > Yea, the BioJava Blast parser has not been maintained in quite a while. > Probably parsing the XML output of Blast is the thing to do nowadays. About > Biojava3: the wiki documentation is a bit behind, the code is now in the > main biojava-trunk and development has been quite active over the last > months. > > Andreas > > On Tue, Mar 16, 2010 at 2:20 AM, Louise Ott <[email protected]> wrote: > > > > > > > Hello, > > I tried to use the biojava blast parser myself but i didn't find a way to > > get back these informations.If your blast result can be in xml, you > should > > try to use jaxb to parse it (this is what i used).There are already some > > code for marshall/unmarshall in the biojava3 project.I give you the link, > > but it seems to be dead right now : > > > > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/branches/biojava3 > > http://www.biojava.org/wiki/BioJava3_project > > Have a nice day, > > Louise > > > > > > > Date: Mon, 15 Mar 2010 19:09:50 -0400 > > > From: [email protected] > > > To: [email protected] > > > Subject: [Biojava-l] question about BLAST output parsing > > > > > > Hi, > > > > > > Thanks advance for help. > > > > > > For the following piece of text appearing in a blast output. How can I > > get > > > the fields of "Identities", "Positives", "Gaps" as well as the > alignment > > > information, such as "DK V L+D + G +S + +++ +E GA+K+ L + AAPE" and > > > subject string? > > > > > > >sp|B9KAQ6.1|UPP_THENN RecName: Full=Uracil phosphoribosyltransferase; > > > AltName: Full=UMP > > > pyrophosphorylase; AltName: Full=UPRTase > > > Length = 209 > > > > > > Score = 32.0 bits (71), Expect = 9.7, Method: Compositional matrix > > > adjust. > > > Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 2/42 (4%) > > > > > > Query: 360 DKNVLLVDDSIVRGTTSEQIIEMAREAGAKKVYLAS--AAPE 399 > > > DK V L+D + G +S + +++ +E GA+K+ L + AAPE > > > Sbjct: 124 DKEVFLLDPMLATGVSSVKALDILKENGARKITLVALIAAPE 165 > > > _______________________________________________ > > > Biojava-l mailing list - [email protected] > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > _________________________________________________________________ > > Hotmail arrive sur votre téléphone ! Compatible Iphone, Windows Phone, > > Blackberry, … > > http://www.messengersurvotremobile.com/?d=Hotmail > > _______________________________________________ > > 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
