net.maizegenetics.pangenome.trimAnchors

Class TrimGenotypeTableAnchors

java.lang.Object

net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors

public class TrimGenotypeTableAnchors
extends Object

Simple class holding utilities to trim a genotype table by identity and coverage thresholds TODO needs to be refractored and have a standardized api Created by zrm22 on 7/6/17.

Method Summary

Modifier and Type	Method and Description
static net.maizegenetics.dna.snp.GenotypeTable	createTrimmedFastaGenotypeTable(String fastaFileName, String refTaxaName, double idThreshold, double coverageThreshold, int leftTrimStart, int rightTrimStart, int consecFailingThresholds, int consecPassingThresholds) Method which will create a trimmed GenotypeTable based on the gene start and end positions
static net.maizegenetics.dna.snp.GenotypeTable	createTrimmedFastaGenotypeTable(String fastaFileName, String refTaxaName, String chr, int startPos, double idThreshold, double coverageThreshold, int leftTrimStart, int rightTrimStart, int consecFailingThresholds, int consecPassingThresholds) Method which will create a trimmed GenotypeTable based on the gene start and end positions

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

createTrimmedFastaGenotypeTable

public static net.maizegenetics.dna.snp.GenotypeTable createTrimmedFastaGenotypeTable(String fastaFileName,
                                                                                      String refTaxaName,
                                                                                      double idThreshold,
                                                                                      double coverageThreshold,
                                                                                      int leftTrimStart,
                                                                                      int rightTrimStart,
                                                                                      int consecFailingThresholds,
                                                                                      int consecPassingThresholds)

Method which will create a trimmed GenotypeTable based on the gene start and end positions

Parameters:

fastaFileName - Import fasta file to be read.

refTaxaName - Name of the Reference taxa(ex B73Ref) which is a row in the fasta file.

idThreshold - Percentage of Identity which needs to be met to be considered conserved.

coverageThreshold - Percentage of Coverage across all lines in the fasta file which needs to be met to be considered conserved.

leftTrimStart - Start point for the left direction trimming. Generally this is the gene start.

rightTrimStart - Start point for the right direction trimming. Generally this is the gene end.

consecFailingThresholds - Number of consecutive base pairs which need to fail to stop growing the region and start walking back to the gene bounds.

consecPassingThresholds - Number of consecutive base pairs which need to pass the thresholds to stop shrinking the region and stop trimming.

Returns:

GenotypeTable which is trimmed by the input parameters

createTrimmedFastaGenotypeTable

public static net.maizegenetics.dna.snp.GenotypeTable createTrimmedFastaGenotypeTable(String fastaFileName,
                                                                                      String refTaxaName,
                                                                                      String chr,
                                                                                      int startPos,
                                                                                      double idThreshold,
                                                                                      double coverageThreshold,
                                                                                      int leftTrimStart,
                                                                                      int rightTrimStart,
                                                                                      int consecFailingThresholds,
                                                                                      int consecPassingThresholds)

Method which will create a trimmed GenotypeTable based on the gene start and end positions

Parameters:

fastaFileName - Import fasta file to be read.

refTaxaName - Name of the Reference taxa(ex B73Ref) which is a row in the fasta file.

chr - Name of the chromosome we need for the GenotypeTable

startPos - Start position of the reference sequence so we can annotate the Position list

idThreshold - Percentage of Identity which needs to be met to be considered conserved.

coverageThreshold - Percentage of Coverage across all lines in the fasta file which needs to be met to be considered conserved.

leftTrimStart - Start point for the left direction trimming. Generally this is the gene start.

rightTrimStart - Start point for the right direction trimming. Generally this is the gene end.

consecFailingThresholds - Number of consecutive base pairs which need to fail to stop growing the region and start walking back to the gene bounds.

consecPassingThresholds - Number of consecutive base pairs which need to pass the thresholds to stop shrinking the region and stop trimming.

Returns:

GenotypeTable which is trimmed by the input parameters