public final class ReferenceDictParser extends Object
ReferenceDictParser
from UCSC and RefSeq data.
The mapping between chromosome names and RefSeq/GeneBank IDs is done using a RefSeq "chr_accessions_*" file and the
chromosome information is retrieved from the UCSC chromInfo.txt.gz file.Constructor and Description |
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ReferenceDictParser(String chromInfoPath,
String chrAccessionsPath,
org.ini4j.Profile.Section iniSection)
Initialize the parser with the paths to the file to parse.
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Modifier and Type | Method and Description |
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ReferenceDictionary |
parse()
Load accessions and chromInfo file and return resulting ReferenceDictionary.
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public ReferenceDictParser(String chromInfoPath, String chrAccessionsPath, org.ini4j.Profile.Section iniSection)
chromInfoPath
- path to knownGene.txt.gz file.chrAccessionsPath
- path to "chr_accessions_*" file.iniSection
- Profile.Section
with configuration from INI filepublic ReferenceDictionary parse() throws TranscriptParseException
ReferenceDictionary
TranscriptParseException
- on problems loading or parsing dataCopyright © 2016. All rights reserved.