[Biojava-dev] [Bug 2536] New: GenBankFormat Doesn't Support Bond Features

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2536

           Summary: GenBankFormat Doesn't Support Bond Features
           Product: BioJava
           Version: 1.5
          Platform: All
        OS/Version: Windows
            Status: NEW
          Severity: major
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: 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


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