Uses of Class
org.snpeff.snpEffect.factory.SnpEffPredictorFactory

Packages that use SnpEffPredictorFactory
Package
Description
 
  • Uses of SnpEffPredictorFactory in org.snpeff.snpEffect.factory

    Modifier and Type
    Class
    Description
    class 
    This class creates a SnpEffectPredictor from an Embl file.
    class 
    This class creates a SnpEffectPredictor from a 'features' file.
    class 
    This class creates a SnpEffectPredictor from a GenBank file.
    class 
    This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration The files used are: - genes.txt : Biomart query from Ensembl (see scripts/genes_dataset.xml) - Fasta files: One per chromosome (as described in the config file)
    class 
    This class creates a SnpEffectPredictor from a GFF file.
    class 
    This class creates a SnpEffectPredictor from a GFF2 file.
    class 
    This class creates a SnpEffectPredictor from a GFF3 file References: - http://www.sequenceontology.org/gff3.shtml - http://gmod.org/wiki/GFF3 - http://www.eu-sol.net/science/bioinformatics/standards-documents/gff3-format-description
    class 
    This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html
    class 
    This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser Fields in this table Field Example SQL type Info Description ----- ------- -------- ---- ----------- name uc001aaa.3 varchar(255) values Name of gene chrom chr1 varchar(255) values Reference sequence chromosome or scaffold strand + char(1) values + or - for strand txStart 11873 int(10) unsigned range Transcription start position txEnd 14409 int(10) unsigned range Transcription end position cdsStart 11873 int(10) unsigned range Coding region start cdsEnd 11873 int(10) unsigned range Coding region end exonCount 3 int(10) unsigned range Number of exons exonStarts 11873,12612,13220, longblob Exon start positions exonEnds 12227,12721,14409, longblob Exon end positions proteinID varchar(40) values UniProt display ID for Known Genes, UniProt accession or RefSeq protein ID for UCSC Genes alignID uc001aaa.3 varchar(255) values Unique identifier for each (known gene, alignment position) pair
    class 
    This class creates a random set of chromosomes, genes, transcripts and exons
    class 
    This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser RefSeq table schema: http://genome.ucsc.edu/cgi-bin/hgTables field example SQL type info description bin 585 smallint(5) range Indexing field to speed chromosome range queries.