Class GtfReporterImporter

All Implemented Interfaces:
AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample, WrappedConfigureByExample

public class GtfReporterImporter extends ReporterFlatFileImporter implements WrappedConfigureByExample
Reporter importer implementation that create reporters from information in GTF files. The implementation builds on the regular ReporterFlatFileImporter but uses a GtfInputStream as a wrapper to generate a pure column-based output which can be used by the regular tools for file parsing. The importer will also skip lines with a non-unique transcript_id+seqname.

The default configuration is to use the transcript_id+seqname as the reporter id and name. gene_id is stored as "gene symbol" and seqname as "chromosome". The default configuration can be changed by user configurations depending on what additional attributes that are present in the GTF file.

Last modified
$Date: 2011-09-29 13:27:33 +0200 (to, 29 sep 2011) $