public class RampSeqAlignFromBlastTags
extends AbstractPlugin
This class takes a rAmpSeq database populated with tags,a reference Genome, a filtered BLAST file output and primers, then: (1) creates reference tags using the blast alignment output (2) runs tag/tag alignment for each tag in the DB, (3) runs tag/refTag alignment for each tag against each ref tag (4) runs refTag/refTag alignment for each refTag in the DB> (5) all alignments are stored in the db tagAlignments table. Alignments are performed and stored in groups to prevent overwhelming the DB with massive load commands. Blast was run on CBSU using these parameters: Make the reference files: makeblastdb -dbtype nucl -in -parse_seqids -out maizeAGPV4.db Run blast using maizeAGPV4.db from command above: blastn -num_threads 24 -db maizeAGPV4.db -query anp68R1Tags.fasta -evalue 1e-60 -max_target_seqs 5 -max_hsps 1 -outfmt 6 -out anp68TagsR1Result/blastANP68_R1.txt The blast output file was filtered using the 3 commands below. The first filters identity down to 98 %, the second gets alignment lengths that were at least 148, the 3rd filters it down to just the chrom, start, end positions: awk '$3 >= 98.000 {print $0}' blastANP68_R1.txt > blastANP68_R1_98per.txt awk '$4 >= 148 {print $0}' blastANP68_R1_98per.txt > blastANP68_R1_98per_148align.txt awk {'printf ("%s\t%s\t%s\n", $2, $9, $10)'} blastANP68_R1_98per_148align.txt > blastANP68_R1_98per_148align_3cols.txt It is the last file from awk, blastANP68_R1_98per_148align_3cols.txt, that is given as a parameter here.
public RampSeqAlignFromBlastTags()
public RampSeqAlignFromBlastTags(java.awt.Frame parentFrame)
public RampSeqAlignFromBlastTags(java.awt.Frame parentFrame,
boolean isInteractive)
public void postProcessParameters()
public boolean createRefTagsFromBlast(java.lang.String chromStartEndFile,
java.lang.String forwardP,
java.lang.String reverseP,
com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.map.Position> refTagPositionMap)
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public java.lang.String dBFile()
Input database file with tags and taxa distribution
public RampSeqAlignFromBlastTags dBFile(java.lang.String value)
Set Input DB. Input database file with tags and taxa distribution
value - Input DBpublic java.lang.String refGenome()
Referemce Genome File for aligning against
public RampSeqAlignFromBlastTags refGenome(java.lang.String value)
Set Reference Genome File. Referemce Genome File for aligning against
value - Reference Genome Filepublic java.lang.Integer minTagCount()
Minimum count of reads for a tag to be aligned
public RampSeqAlignFromBlastTags minTagCount(java.lang.Integer value)
Set Min Tag Count. Minimum count of reads for a tag to be aligned
value - Min Tag Countpublic java.lang.Integer match_reward()
Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
public RampSeqAlignFromBlastTags match_reward(java.lang.Integer value)
Set Match Reward Amount. Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
value - Match Reward Amountpublic java.lang.Integer mismatch_penalty()
Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
public RampSeqAlignFromBlastTags mismatch_penalty(java.lang.Integer value)
Set Mismatch Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
value - Mismatch Penalty Amountpublic java.lang.Integer gap_penalty()
Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
public RampSeqAlignFromBlastTags gap_penalty(java.lang.Integer value)
Set Gap Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
value - Gap Penalty Amountpublic java.lang.String forwardp()
String containing the forward primer sequence.
public RampSeqAlignFromBlastTags forwardp(java.lang.String value)
Set Forward Primer. String containing the forward primer sequence.
value - Forward Primerpublic java.lang.String reversep()
String containing the reverse primer sequence.
public RampSeqAlignFromBlastTags reversep(java.lang.String value)
Set Reverse Primer. String containing the reverse primer sequence.
value - Reverse Primerpublic java.lang.String blastFile()
Tab delimited Blast file output with NO header line, that contains only the data from columns for chrom, start postion, end position. This data should be filtered to contain only entries whose identiy value was 98% or greater.
public RampSeqAlignFromBlastTags blastFile(java.lang.String value)
Set Blast File. Tab delimited Blast file output with NO header line, that contains only the data from columns for chrom, start position, end position. This data should be filtered to contain only entries whose identify value was 98% or greater.
value - Blast File