trans.tpmap
Class TPMapOligoBlastFilter

java.lang.Object
  trans.tpmap.TPMapOligoBlastFilter

public class TPMapOligoBlastFilter

extends java.lang.Object

Application for remapping and filtering a text version bpmap file with BLAST. This is wickedly slow :( ! Can't use -B or megablast so stuck with this junk. If you don't care about mismatches then use the MummerFilter applicaiton. Filters a tpmap file only printing out oligo lines that have one unique match to the sequenced genome. The orientation direction is replaced with the number of 1bp matches for files appended with Bls or total number of matches (1bp + exact) for files appended with NoTrmBls. To launch on Sapo cluster: java -Xmx1500M nix/util/gen/JQSub cd /home/sapo/nix/NixSourceCode/ return java -Xmx1500M nix/affy/TPMapOligoBlastFilter -d /home/sapo/nix/Affy/BLAST/whole_genome.fasta -s /home/sapo/software/seqanal/alignment/ncbi/bin/blastall -b /home/sapo/nix/Affy/TPMap/Extra/extra.tpmap

Constructor Summary

TPMapOligoBlastFilter(java.lang.String[] args)

Method Summary

static BlastFilterResult	blastForOneBPRepeats(java.lang.String blastAll, java.lang.String database, java.io.File fastaFile) This has been tweaked to find 1bp mismatches in a 25mer to a genome.
static void	main(java.lang.String[] args)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles

Methods inherited from class java.lang.Object

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

Constructor Detail

TPMapOligoBlastFilter

public TPMapOligoBlastFilter(java.lang.String[] args)

Method Detail

blastForOneBPRepeats

public static BlastFilterResult blastForOneBPRepeats(java.lang.String blastAll,
                                                     java.lang.String database,
                                                     java.io.File fastaFile)

This has been tweaked to find 1bp mismatches in a 25mer to a genome. No indels. Returns the number of matches found in the database, thus a unique oligo would be found once. Returns -1 if something went wrong. Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start,q. end, s. start, s. end, e-value, bit score 0 1 2 3 4 5 6 7 8 9 10 11

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign any new varibles

printDocs

public static void printDocs()

main

public static void main(java.lang.String[] args)