I added a new patch that actually fixes the problem (you really should halt your build when a test case fails by the way :). Basically, it just skips over "Bond" features.
On Thu, Jul 3, 2008 at 2:52 PM, James Carman <[EMAIL PROTECTED]> wrote: > Richard, > > I filed the BugZilla issue: > > http://bugzilla.open-bio.org/show_bug.cgi?id=2536 > > I also attached a patch that I believe fixes the issue (it includes a > test case). I hope that helps! > > James > > On Thu, Jul 3, 2008 at 11:19 AM, James Carman > <[EMAIL PROTECTED]> wrote: >> Ok, great! I just wanted to make sure I wasn't doing something >> stupid! :) I'll file the BugZilla issue now (and download the source >> so that I can hopefully provide a patch). >> >> On Thu, Jul 3, 2008 at 11:17 AM, Richard Holland >> <[EMAIL PROTECTED]> wrote: >>> 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
