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comparison Dotplot_Release/BaitCheck.pl @ 0:dfa3436beb67 draft

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author bornea
date Fri, 29 Jan 2016 09:56:02 -0500
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-1:000000000000 0:dfa3436beb67
1 #!/usr/bin/perl
2
3 # 27/04/2014
4
5 if($#ARGV==0){
6 print "This program checks the number of baits in a Saint Output File.\n";
7 print "\nusage:\n $0\n-i [csv saint output file]]\n\n";
8 die;
9 }
10 else{
11 $i=0;
12 $cutoff=0.01;
13 while($i<=$#ARGV){
14 if($ARGV[$i] eq '-i'){
15 $i++;
16 $ifile=$ARGV[$i];
17 }
18 else{
19 die "\Incorrect program usage\n\n";
20 }
21 $i++;
22 }
23 }
24
25 $file='';
26 open(IFILE,"<$ifile") || die "$ifile can't be opened: $!";
27 { local $/=undef; $file=<IFILE>; }
28 @lines=split /[\r\n]+/, $file;
29 foreach $line (@lines) {
30 if($line =~ /^Bait/){
31 }
32 elsif($line =~ /^([^\t]+)/){
33 if($1 ne $bait[$baitn]){
34 $baitn++;
35 $bait[$baitn]=$1;
36 }
37 }
38 else{
39 }
40 }
41 close(IFILE);
42
43 print $baitn;
44
45