Class
UcscRecordRepresent the information for one UCSC gene annotation record.
Represent the information for one UCSC gene annotation record.
Implements | FormattedFileRecordConcept |
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All Impl'd | AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, FormattedFileRecordConcept |
Defined in | <seqan/ucsc_io.h> |
Signature |
class UcscRecord;
|
Interface Function Overview
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void clear(record);
Clear UcscRecord.
Interface Functions Inherited From AssignableConcept
Member Variable Overview
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uint32_t UcscRecord::annotationBeginPos
Start of the annotation (0-based, defaults to -1). -
CharString UcscRecord::annotationEndPos
End position of the annotation, defaults to -1. -
int32_t UcscRecord::cdsBegin
Start of the coding region (0-based position, defaults to -1). -
int32_t UcscRecord::cdsEnd
End of the coding region, defaults to -1. -
CharString UcscRecord::contigName
Name of the contig of the genomic location. -
CharString UcscRecord::exonBegin
Start of the exon (0-based position, defaults to -1). -
CharString UcscRecord::exonEnds
End of the exon, defaults to -1. -
CharString UcscRecord::proteinName
Name of the coded protein. -
CharString UcscRecord::transName
Name of the transcript.
Detailed Description
The UCSC genome browser server allows the download of a set of the known genes and isoforms used in the browser. These files can be downloaded from the UCSC FTP's goldenPath folder, e.g. the one for hg19.
To load the annotations, you need to download both the knownGenes.txt.gz and the knownIsoforms.txt.gz files from the UCSC goldenPath database. These files can then be read record by record into a UcscRecord. This record type is capable of representing records from either file type.
Interface Functions Detail
void clear(record);
Clear UcscRecord.
Parameters
record
|
The UcscRecord to clear. |
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Clears all strings and resets it to default initialization state.
Data Races
Thread safety unknown!
Member Variables Detail
uint32_t UcscRecord::annotationBeginPos
Start of the annotation (0-based, defaults to -1).
CharString UcscRecord::annotationEndPos
End position of the annotation, defaults to -1.
int32_t UcscRecord::cdsBegin
Start of the coding region (0-based position, defaults to -1).
int32_t UcscRecord::cdsEnd
End of the coding region, defaults to -1.
CharString UcscRecord::contigName
Name of the contig of the genomic location.
CharString UcscRecord::exonBegin
Start of the exon (0-based position, defaults to -1).
CharString UcscRecord::exonEnds
End of the exon, defaults to -1.
CharString UcscRecord::proteinName
Name of the coded protein.
CharString UcscRecord::transName
Name of the transcript.