[Biojava-l] ParseException: Could not understand position: bond(39, 96

[Richard Holland]

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 <james at carmanconsulting.com>:
> 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?
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