Apparently not. I don't think they're part of the formal Genbank specification, or at least not the one that was current at the time the parser was written (in 2004). If they were, then we must have missed them out by accident. Sorry! Could you raise a bug report via BugZilla onthe BioJava website and someone will look into it as soon as they get a chance.
cheers, Richard 2008/7/3 James Carman <[EMAIL PROTECTED]>: > I'm trying to parse the file: > > ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian12.protein.gpff.gz > > using: > > RichSequence.IOTools.readGenbankProtein() > > and I keep getting this error (the date column is from my build server > which runs this "loader", sorry): > > [10:51:36]: org.biojava.bio.BioException: Could not read sequence > [10:51:36]: at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) > [10:51:36]: at > com.pg.iip.loader.pubrec.RefSeqLoader.loadPublicRecords(RefSeqLoader.java:106) > [10:51:36]: at > com.pg.iip.loader.pubrec.PublicRecordLoader.doLoad(PublicRecordLoader.java:248) > [10:51:36]: at > com.pg.iip.loader.AbstractLoader.execute(AbstractLoader.java:56) > [10:51:36]: at > com.pg.iip.loader.LoaderUtils.executeLoader(LoaderUtils.java:20) > [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > [10:51:36]: at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > [10:51:36]: at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > [10:51:36]: at java.lang.reflect.Method.invoke(Method.java:585) > [10:51:36]: at > com.pg.iip.loader.plugin.RunLoaderMojo.invoke(RunLoaderMojo.java:95) > [10:51:36]: at > com.pg.iip.loader.plugin.RunLoaderMojo.execute(RunLoaderMojo.java:142) > [10:51:36]: at > org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:447) > [10:51:36]: at > org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:539) > [10:51:36]: at > org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:493) > [10:51:36]: at > org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:463) > [10:51:36]: at > org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:311) > [10:51:36]: at > org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:278) > [10:51:36]: at > org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:143) > [10:51:36]: at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:333) > [10:51:36]: at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:126) > [10:51:36]: at org.apache.maven.cli.MavenCli.main(MavenCli.java:282) > [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > [10:51:36]: at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > [10:51:36]: at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > [10:51:36]: at java.lang.reflect.Method.invoke(Method.java:585) > [10:51:36]: at > org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) > [10:51:36]: at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) > [10:51:36]: at > org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) > [10:51:36]: at org.codehaus.classworlds.Launcher.main(Launcher.java:375) > [10:51:36]: Caused by: org.biojava.bio.seq.io.ParseException: Could > not understand position: bond(39,96 > [10:51:36]: at > org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285) > [10:51:36]: at > org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:271) > [10:51:36]: at > org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:131) > [10:51:36]: at > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:490) > [10:51:36]: at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) > [10:51:36]: ... 28 more > > Does the parser not understand "Bond" features? > _______________________________________________ > 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
