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

[James Carman]

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