Skip to content

make or read genbank file error when feature spans zero point of circular sequence #855

@chenzhiw

Description

@chenzhiw

Download a genbank file from this page.
Read it with biojava and error as below:

Exception in thread "main" java.lang.IllegalStateException: Start (7028) is greater than end (286); this is an incorrect format
at org.biojava.nbio.core.sequence.location.template.AbstractLocation.assertLocation(AbstractLocation.java:133)
at org.biojava.nbio.core.sequence.location.template.AbstractLocation.(AbstractLocation.java:119)
at org.biojava.nbio.core.sequence.location.template.AbstractLocation.(AbstractLocation.java:92)
at org.biojava.nbio.core.sequence.location.SimpleLocation.(SimpleLocation.java:64)
at org.biojava.nbio.core.sequence.location.SimpleLocation.(SimpleLocation.java:55)
at org.biojava.nbio.core.sequence.location.InsdcParser.parseLocationString(InsdcParser.java:241)
at org.biojava.nbio.core.sequence.location.InsdcParser.parseLocationString(InsdcParser.java:189)
at org.biojava.nbio.core.sequence.location.InsdcParser.parse(InsdcParser.java:143)
at org.biojava.nbio.core.sequence.io.GenbankSequenceParser.parse(GenbankSequenceParser.java:283)
at org.biojava.nbio.core.sequence.io.GenbankSequenceParser.getSequence(GenbankSequenceParser.java:402)
at org.biojava.nbio.core.sequence.io.GenbankReader.process(GenbankReader.java:153)
at org.biojava.nbio.core.sequence.io.GenbankReader.process(GenbankReader.java:121)
at org.biojava.nbio.core.sequence.io.GenbankReaderHelper.readGenbankDNASequence(GenbankReaderHelper.java:178)
at org.biojava.nbio.core.sequence.io.GenbankReaderHelper.readGenbankDNASequence(GenbankReaderHelper.java:190)

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions