class |
SnpEffPredictorFactoryEmbl |
This class creates a SnpEffectPredictor from an Embl file.
|
class |
SnpEffPredictorFactoryFeatures |
This class creates a SnpEffectPredictor from a 'features' file.
|
class |
SnpEffPredictorFactoryGenBank |
This class creates a SnpEffectPredictor from a GenBank file.
|
class |
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)
|
class |
SnpEffPredictorFactoryGff |
This class creates a SnpEffectPredictor from a GFF file.
|
class |
SnpEffPredictorFactoryGff2 |
This class creates a SnpEffectPredictor from a GFF2 file.
|
class |
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
|
class |
SnpEffPredictorFactoryGtf22 |
This class creates a SnpEffectPredictor from a GTF 2.2 file
References: http://mblab.wustl.edu/GTF22.html
|
class |
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
|
class |
SnpEffPredictorFactoryRand |
This class creates a random set of chromosomes, genes, transcripts and exons
|
class |
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.
|