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1 #!/usr/bin/perl -w
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2 # Author: Thomas Thiel
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3 # Program name: prim_output.pl
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4 # Description: converts the Primer3 output into an table
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5
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6 open (SRC,"<$ARGV[0]") || die ("\nError: Couldn't open Primer3 results file (*.p3out) !\n\n");
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7 my $filename = $ARGV[0];
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8 $filename =~ s/\.p3out//;
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9 open (IN,"<$ARGV[1]") || die ("\nError: Couldn't open source file containing MISA (*.misa) results !\n\n");
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10 open (OUT,">$ARGV[2]") || die ("nError: Couldn't create file !\n\n");
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11
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12 my ($seq_names_failed,$count_failed,$count);
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13 print OUT "ID\tSSR nr.\tSSR type\tSSR\tsize\tstart\tend\t";
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14 print OUT "FORWARD PRIMER1 (5'-3')\tTm(°C)\tsize\tREVERSE PRIMER1 (5'-3')\tTm(°C)\tsize\tPRODUCT1 size (bp)\tstart (bp)\tend (bp)\t";
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15 print OUT "FORWARD PRIMER2 (5'-3')\tTm(°C)\tsize\tREVERSE PRIMER2 (5'-3')\tTm(°C)\tsize\tPRODUCT2 size (bp)\tstart (bp)\tend (bp)\t";
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16 print OUT "FORWARD PRIMER3 (5'-3')\tTm(°C)\tsize\tREVERSE PRIMER3 (5'-3')\tTm(°C)\tsize\tPRODUCT3 size (bp)\tstart (bp)\tend (bp)\n";
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17
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18 undef $/;
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19 my $in = <IN>;
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20 study $in;
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21
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22 $/ = "=\n";
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23
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24 while (<SRC>)
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25 {
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26 my ($id,$ssr_nr) = (/PRIMER_SEQUENCE_ID=(\S+)_(\d+)/);
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27
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28 $in =~ /($id\t$ssr_nr\t.*)\n/;
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29 my $misa = $1;
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30
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31 /PRIMER_LEFT_SEQUENCE=(.*)/ || do {$count_failed++;print OUT "$misa\n"; next};
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32 my $info = "$1\t";
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33
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34 /PRIMER_LEFT_TM=(.*)/; $info .= "$1\t";
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35 /PRIMER_LEFT=\d+,(\d+)/; $info .= "$1\t";
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36
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37 /PRIMER_RIGHT_SEQUENCE=(.*)/; $info .= "$1\t";
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38 /PRIMER_RIGHT_TM=(.*)/; $info .= "$1\t";
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39 /PRIMER_RIGHT=\d+,(\d+)/; $info .= "$1\t";
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40
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41 /PRIMER_PRODUCT_SIZE=(.*)/; $info .= "$1\t";
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42 /PRIMER_LEFT=(\d+),\d+/; $info .= "$1\t";
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43 /PRIMER_RIGHT=(\d+),\d+/; $info .= "$1\t";
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44
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45
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46 /PRIMER_LEFT_1_SEQUENCE=(.*)/; $info .= "$1\t";
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47 /PRIMER_LEFT_1_TM=(.*)/; $info .= "$1\t";
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48 /PRIMER_LEFT_1=\d+,(\d+)/; $info .= "$1\t";
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49
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50 /PRIMER_RIGHT_1_SEQUENCE=(.*)/; $info .= "$1\t";
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51 /PRIMER_RIGHT_1_TM=(.*)/; $info .= "$1\t";
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52 /PRIMER_RIGHT_1=\d+,(\d+)/; $info .= "$1\t";
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53
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54 /PRIMER_PRODUCT_SIZE_1=(.*)/; $info .= "$1\t";
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55 /PRIMER_LEFT_1=(\d+),\d+/; $info .= "$1\t";
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56 /PRIMER_RIGHT_1=(\d+),\d+/; $info .= "$1\t";
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57
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58
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59 /PRIMER_LEFT_2_SEQUENCE=(.*)/; $info .= "$1\t";
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60 /PRIMER_LEFT_2_TM=(.*)/; $info .= "$1\t";
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61 /PRIMER_LEFT_2=\d+,(\d+)/; $info .= "$1\t";
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62
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63 /PRIMER_RIGHT_2_SEQUENCE=(.*)/; $info .= "$1\t";
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64 /PRIMER_RIGHT_2_TM=(.*)/; $info .= "$1\t";
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65 /PRIMER_RIGHT_2=\d+,(\d+)/; $info .= "$1\t";
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66
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67 /PRIMER_PRODUCT_SIZE_2=(.*)/; $info .= "$1\t";
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68 /PRIMER_LEFT_2=(\d+),\d+/; $info .= "$1\t";
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69 /PRIMER_RIGHT_2=(\d+),\d+/; $info .= "$1";
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70
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71 $count++;
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72 print OUT "$misa\t$info\n"
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73 };
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74
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75 #print "\nPrimer modelling was successful for $count sequences.\n";
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76 #print "Primer modelling failed for $count_failed sequences.\n";
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