From: Nagarjun V <arj...@gm...> - 2011-02-16 18:04:00
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Hi, Have been testing Minimus2 with blat(instead of nucmer) for some time now. It seems to give me stable results after using a larger overlap. Could somebody please put it into the next build of amos as an alternative to nucmer, so that i can get some feedback? Changes that need to be done are given at the end of the mail. Thanks and Regards, Nagarjun Vijay *Inside the minimus2.acf file:* BINDIR = /usr/local/bin NUCMER = nucmer DELTAFILTER = delta-filter SHOWCOORDS = show-coords BLAT = blat BTON = perl psltoNucmer.pl #------------------------------------------------------------------------------# ## Building AMOS bank & Dumping reads 10: rm -fr $(BANK) 11: $(BINDIR)/bank-transact -c -z -b $(BANK) -m $(TGT) 12: $(BINDIR)/dumpreads $(BANK) -M $(REFCOUNT) > $(REFSEQ) 13: $(BINDIR)/dumpreads $(BANK) -m $(REFCOUNT) > $(QRYSEQ) ## Getting overlaps 20: $(BLAT) $(REFSEQ) $(QRYSEQ) -fastMap -noHead -minIdentity=$(MINID) -tileSize=$(OVERLAP) $(BOUT) 21: $(BTON) $(BOUT) | $(BINDIR)/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > $(COORDS) 22: $(BINDIR)/nucmer2ovl -ignore $(MAXTRIM) -tab $(COORDS) | $(BINDIR)/sort2 > $(OVLTAB) *psltoNucmer.pl* #!/usr/bin/perl open FILE2, "<",$ARGV[0] or die $!; while($z = <FILE2>){ @values=split(/\t/,$z); print $values[15]."\t".$values[16]."\t|\t".$values[11]."\t".$values[12]."\t|\t".abs($values[16]-$values[15])."\t".abs($values[12]-$values[11])."\t|\t".(sprintf "%.2f",(($values[0]+$values[2]+$values[3])*100)/abs($values[12]-$values[11]))."\t|\t".$values[14]."\t".$values[10]."\t|\t".(sprintf "%.2f",(abs($values[16]-$values[15])*100/$values[14]))."\t".(sprintf "%.2f",(abs($values[12]-$values[11])*100/$values[10]))."\t|\t".$values[13]."\t".$values[9]."\n"; }#end of File while loop |