Mercurial > repos > mkhan1980 > ctcf_analysis

comparison check.pl @ 5:1c09a4a56459 draft

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author mkhan1980
date Thu, 25 Apr 2013 11:20:08 -0400
parents ebad609b8a6d
children
comparison
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4:c30f1e611791 5:1c09a4a56459
104 $kount=0; 104 $kount=0;
105 $coun=0; 105 $coun=0;
106 106
107 # Define the pattern for CTCF. Because of pseudocount, a wildcard is allowed at 107 # Define the pattern for CTCF. Because of pseudocount, a wildcard is allowed at
108 #each position. 108 #each position.
109 my $pattern = "[ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC]"; 109 my $pattern = "[ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN][ATGCN]";
110 110
111 # Compare the pattern with the 19 bp nucleotide segments. 111 # Compare the pattern with the 19 bp nucleotide segments.
112 112
113 while($var =~ m/$pattern/gi) 113 while($var =~ m/$pattern/gi)
114 { 114 {