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
