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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Chentt
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4 #Email: chentt@big.ac.cn
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5 #Date: 2014/06/25
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6 #Modified:
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7 #Description: get out larger than cut off sequence
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8 my $version=1.00;
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9
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10 use strict;
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11 use Getopt::Long;
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12 use File::Basename;
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13 use FileHandle;
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14
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15 my %opts;
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16 GetOptions(\%opts,"i=s","o=s","h");
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17 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
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18 &usage;
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19 }
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20
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21 my $outputdir=$opts{'o'};
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22 unless ($outputdir=~/\/$/) {$outputdir .="/";}
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23
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24 ##############################get cmap##################
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25 my %cmap;
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26 open IN,"<$opts{i}";
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27 while (my $aline=<IN>) {
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28 chomp $aline;
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29 next if($aline=~/^\#/);
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30 my @temp=split/\t/,$aline;
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31 $cmap{$temp[0]}=$outputdir.$temp[0];
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32 }
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33 close IN;
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34 ###########################split ma file######################
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35 my %handle;
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36 foreach (keys %cmap) {
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37 my $name=$cmap{$_}.".sam";
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38 open $handle{$_},">$name";
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39 }
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40 open IN,"<$opts{i}";
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41 while (my $aline=<IN>) {
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42 next if($aline=~/^\#/);
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43 chomp $aline;
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44 my @temp=split/\t/,$aline;
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45 $handle{$temp[0]}-> print ($aline,"\n");
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46
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47 }
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48 close IN;
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49 foreach (keys %handle) {close $_;}
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50
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51
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52 sub usage{
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53 print <<"USAGE";
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54 Version $version
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55 Usage:
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56 $0 -i -o
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57 options:
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58 -i input file
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59 -o output file
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60 -h help
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61 USAGE
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62 exit(1);
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63 }
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64
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