# Package org.snpeff.snpEffect.factory

package org.snpeff.snpEffect.factory

Related Packages
Package
Description
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
Classes
Class
Description
SnpEffPredictorFactory
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration
SnpEffPredictorFactoryEmbl
This class creates a SnpEffectPredictor from an Embl file.
SnpEffPredictorFactoryFeatures
This class creates a SnpEffectPredictor from a 'features' file.
SnpEffPredictorFactoryGenBank
This class creates a SnpEffectPredictor from a GenBank file.
SnpEffPredictorFactoryGenesFile
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)
SnpEffPredictorFactoryGff
This class creates a SnpEffectPredictor from a GFF file.
SnpEffPredictorFactoryGff2
This class creates a SnpEffectPredictor from a GFF2 file.
SnpEffPredictorFactoryGff3
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
SnpEffPredictorFactoryGtf22
This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html
SnpEffPredictorFactoryKnownGene
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
SnpEffPredictorFactoryRand
This class creates a random set of chromosomes, genes, transcripts and exons
SnpEffPredictorFactoryRefSeq
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.