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

[James Carman]

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
<james at carmanconsulting.com> 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
> <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
>>>
>>
>