Package ubic.gemma.core.loader.genome

Class BlatResultParser

  • All Implemented Interfaces:
    LineParser<BlatResult>, Parser<BlatResult>
    public class BlatResultParser
extends BasicLineParser<BlatResult>
    Loader to handle results generated by Jim Kent's Blat. The PSL file format is described at ucsc format faq and golden path blat spec. Blank lines are skipped as are valid PSL headers. Target sequences are assumed to be chromosomes. If a chromosome name (chr10 or chr10.fa) is detected, the name is stripped to be a chromosome number only (e.g. 10). Otherwise, the value is used as is. If the query name starts with "target:", this is removed. Results can be filtered by setting the scoreThreshold parameter.
    Author:
    pavlidis

    • Constructor Detail

      • BlatResultParser

        public BlatResultParser()

    • Method Detail

      • cleanUpQueryName

        public static String cleanUpQueryName​(String queryName)

      • getNumSkipped

        public int getNumSkipped()

      • getSearchedDatabase

        public ExternalDatabase getSearchedDatabase()
        Returns:
        the searchedDatabase

      • setSearchedDatabase

        public void setSearchedDatabase​(ExternalDatabase searchedDatabase)
        Parameters:
        searchedDatabase - the searchedDatabase to set

      • getTaxon

        public Taxon getTaxon()
        Returns:
        the taxon

      • setTaxon

        public void setTaxon​(Taxon taxon)
        Parameters:
        taxon - the taxon to set

      • parseOneLine

        public BlatResult parseOneLine​(String line)
        Description copied from interface: LineParser
        Handle the parsing of a single line from the input.
        Parameters:
        line - line to parse
        Returns:
        parsed object

      • setScoreThreshold

        public void setScoreThreshold​(double score)
        Parameters:
        score - Define a threshold, below which results are ignored. By default all results are read in.