Mercurial > repos > big-tiandm > mirplant2

comparison rfam.pl @ 44:0c4e11018934 draft

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Uploaded
author big-tiandm
date Thu, 30 Oct 2014 21:29:19 -0400
parents 9ae0d25e4169
children c75593f79aa9
comparison
equal deleted inserted replaced
43:4c0b1a94b882 44:0c4e11018934
45 &checkACGT($rfam); 45 &checkACGT($rfam);
46 `bowtie-build $rfam $rfam`; 46 `bowtie-build $rfam $rfam`;
47 $index="$rfam"; 47 $index="$rfam";
48 } 48 }
49 ### genome mapping 49 ### genome mapping
50 `bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt`; 50 `bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt 2> run.log`;
51 51
52 sub checkACGT{ 52 sub checkACGT{
53 my $string; 53 my $string;
54 open IN,"<$rfam"; 54 open IN,"<$rfam";
55 while (my $aline=<IN>) { 55 while (my $aline=<IN>) {