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
