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1 #!/usr/bin/perl
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2
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3 use strict;
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4
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5 my $scaffolds= $ARGV[0];
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6 my $reference = $ARGV[1];
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7 my $output = $ARGV[2];
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8 my $output2 = $ARGV[3];
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9
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10 my $tmpdir = "tmpdir$$";
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11
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12 mkdir($tmpdir);
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13
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14
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15 my ($sc) = split(",",$scaffolds);
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16 $scaffolds = $sc;
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17
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18 system("cp -rf $scaffolds $tmpdir/scaffolds.fa");
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19 system("cp -rf $reference $tmpdir/reference.fa");
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20 chdir($tmpdir);
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21 system("ragoo.py scaffolds.fa reference.fa");
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22
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23
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24 my %hash;
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25 my $id;
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26 open(F,"ragoo_output/ragoo.fasta");
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27 while(<F>){
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28 if (/>(.*)/){$id = $1;}
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29 else{
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30 $hash{$id}.= $_;
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31 }
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32 }
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33 close(F);
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34
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35 open(O,">$output");
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36 foreach my $id(keys(%hash)){
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37 print O ">$id\n";
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38 my $seq = $hash{$id};
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39 for (my $i =0; $i <= length($seq); $i =$i+80){
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40 my $subseq = substr($seq,$i,80);
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41 print O "$subseq\n";
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42 }
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43 }
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44 close(O);
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45
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46 open(O,">$output2");
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47 foreach my $id(keys(%hash)){
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48 if ($id =~/Chr0_RaGOO/){
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49 next;
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50 }
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51 print O ">$id\n";
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52 my $seq = $hash{$id};
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53 for (my $i =0; $i <= length($seq); $i =$i+80){
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54 my $subseq = substr($seq,$i,80);
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55 print O "$subseq\n";
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56 }
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57 }
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58 close(O);
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