public class ColumnsToBinaryFullGenomeTablePlugin
extends AbstractPlugin
This plugin is copied from the ColumnsToBinarySNPOnlyTablePlugin (which was copied Kelly's ColumnsToBinaryPlugin, which re-worked various lynn methods) to create binary files for loading into the hmp321_snp table in the maizeFullGEnomeDB of the Rare Alleles monetdb instance. THe difference between this plugin and the ColumnsToBinarySNPOnlyTablePlugin is the latter creates entries only for identified hmp321 SNPs This method (ColumnsToBinaryFullGenomePlugin) creates entries for all positions listed in in the reference genome. To be consistent with the existing columns in monetdb maize tables, the reference file must be a link to a copy of the Zea_mays.AGPv3.20.dna.genome.fa file stored on andersonii in Research/Zea/Genotypes/Annotations/monetDB/refGenomeFiles. The "inputFile" parameter can be either a single file containing data for all chromosomes or a directory of files split by chromosome. If all chroms are in a single file, that file must be sorted by chromosome and position, and must contain a header line that contains the columns "chr" and "pos" along with user specified data columns. If the "inputFile" parameter is a directory, the only *.txt files it holds must be files intended for this processing. These files must be split by chromosome and must be named such that they will sort lexicographically in chromosome order. For example: files named chr01.txt, chr02.txt ... chr09.txt, chr10.txt will sort from 1-10. But files named chr1.txt, chr2,txt ... chr9.txt, chr10.txt will not. In the latter case, chr10.txt will be processed before the other files. This plugin may also be used to create binaries for the maizeChrom10DB. In this case, we still use the full reference genome, but only chrom 10 is processed. The inputFile paramaeter shoudl be just 1 file containing chromosome 10 data.
public ColumnsToBinaryFullGenomeTablePlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public ColumnsToBinaryFullGenomeTablePlugin()
protected void preProcessParameters(DataSet input)
protected void postProcessParameters()
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public static void main(java.lang.String[] args)
public java.lang.String inputFile()
File or a Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!
public ColumnsToBinaryFullGenomeTablePlugin inputFile(java.lang.String value)
Set Input Directory. Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!
value - Input Directory or Filepublic java.lang.String refFile()
Link to maize reference file.
public ColumnsToBinaryFullGenomeTablePlugin refFile(java.lang.String value)
Set refFile.
value - refFilepublic java.lang.String outBase()
Output directory and base filename to hold the binary files. Will make directory if neccesary
public ColumnsToBinaryFullGenomeTablePlugin outBase(java.lang.String value)
Set outBase. Output directory and base filename to hold the binary files. Will make directory if neccesary
value - outBasepublic java.lang.String colsFloat()
Comma separated list of column names to generate real binaries for
public ColumnsToBinaryFullGenomeTablePlugin colsFloat(java.lang.String value)
Set Columns keep as Real (Float). Comma separated list of column names to generate real binaries for
value - Columns keep as Real (Float)public java.lang.String colsInt()
Comma separated list of column names to generate int binaries for
public ColumnsToBinaryFullGenomeTablePlugin colsInt(java.lang.String value)
Set Columns keep as Int. Comma separated list of column names to generate int binaries for
value - Columns keep as Intpublic java.lang.String colsShort()
Comma separated list of column names to generate short binaries for
public ColumnsToBinaryFullGenomeTablePlugin colsShort(java.lang.String value)
Set Columns keep as Short. Comma separated list of column names to generate short binaries for
value - Columns keep as Shortpublic java.lang.String colsLong()
Comma separated list of column names to generate long binaries for
public ColumnsToBinaryFullGenomeTablePlugin colsLong(java.lang.String value)
Set Columns keep as Long. Comma separated list of column names to generate long binaries for
value - Columns keep as Longpublic java.lang.String colsByte()
Comma separated list of column names to generate byte binaries for
public ColumnsToBinaryFullGenomeTablePlugin colByte(java.lang.String value)
Set Columns keep as Byte. Comma separated list of column names to generate byte binaries for
value - Columns keep as bhtepublic java.lang.String colsAllele()
Comma separated list of column names to generate byte binaries for
public ColumnsToBinaryFullGenomeTablePlugin colsAllele(java.lang.String value)
Set Columns translate allele values to 0-5. Comma separated list of column names of single character alleles to be translated from A/C/G/T/+/- to 0-5.
value - Columns keep for translated alleles stored as bytespublic java.lang.String colsChar()
Comma separated list of column names to generate char binaries for
public ColumnsToBinaryFullGenomeTablePlugin colsChar(java.lang.String value)
Set Columns keep as Char. Comma separated list of column names to generate char binaries for
value - Columns keep as Charpublic java.lang.String colsLog10()
Comma separated list of column names to first transform using -log10 then generate binaries for
public ColumnsToBinaryFullGenomeTablePlugin colsLog10(java.lang.String value)
Set Columns to Keep and transform -log10. Comma separated list of column names to first transform using -log10 then generate binaries for
value - Columns to Keep and transform -log10public java.lang.Boolean range()
Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'
public ColumnsToBinaryFullGenomeTablePlugin range(java.lang.Boolean value)
Set Range information?. Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'
value - Range information?public java.lang.Boolean negToZero()
Will set negative float denoted column values to zero (otherwise they are set to Float.MIN
public ColumnsToBinaryFullGenomeTablePlugin negToZero(java.lang.Boolean value)
Set Negative floats to zero?. Will set negative float denoted column values to zero (otherwise they are set to Float.MIN
value - Negative floats to zero?public java.lang.Boolean missToZero()
Will set missing float denoted column values to zero (otherwise they are set to Float.MIN
public ColumnsToBinaryFullGenomeTablePlugin missToZero(java.lang.Boolean value)
Set Missing float values to zero?. Will set missing float denoted column values to zero (otherwise they are set to Float.MIN
value - Missing float values to zero?public java.lang.Boolean oneBased()
Will assume positions and ranges are 1-based unless otherwise set.
public ColumnsToBinaryFullGenomeTablePlugin oneBased(java.lang.Boolean value)
Set positions to 1-based unless this variable is "false".
value - 1-based positions?