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

[James Carman]

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
<dicknetherlands at gmail.com> 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 <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?
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>