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0
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1 #!/usr/bin/perl
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2
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3 use strict;
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1
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4 use File::Basename;
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5 my $dirname = dirname(__FILE__);
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0
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6
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7 my $scaffolds= $ARGV[0];
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8 my $reference = $ARGV[1];
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9 my $output = $ARGV[2];
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10 my $output2 = $ARGV[3];
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11
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12 my $tmpdir = "tmpdir$$";
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13
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14 mkdir($tmpdir);
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15
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16
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17 my ($sc) = split(",",$scaffolds);
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18 $scaffolds = $sc;
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19
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20 system("cp -rf $scaffolds $tmpdir/scaffolds.fa");
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21 system("cp -rf $reference $tmpdir/reference.fa");
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22 chdir($tmpdir);
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3
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23 system("$dirname/ragoo.py scaffolds.fa reference.fa >>$output 2>&1");
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0
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24
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25
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26 my %hash;
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27 my $id;
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28 open(F,"ragoo_output/ragoo.fasta");
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29 while(<F>){
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30 if (/>(.*)/){$id = $1;}
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31 else{
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32 $hash{$id}.= $_;
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33 }
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34 }
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35 close(F);
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36
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3
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37 open(O,">>$output");
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0
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38 foreach my $id(keys(%hash)){
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39 print O ">$id\n";
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40 my $seq = $hash{$id};
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41 for (my $i =0; $i <= length($seq); $i =$i+80){
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42 my $subseq = substr($seq,$i,80);
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43 print O "$subseq\n";
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44 }
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45 }
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46 close(O);
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47
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48 open(O,">$output2");
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49 foreach my $id(keys(%hash)){
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50 if ($id =~/Chr0_RaGOO/){
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51 next;
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52 }
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53 print O ">$id\n";
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54 my $seq = $hash{$id};
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55 for (my $i =0; $i <= length($seq); $i =$i+80){
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56 my $subseq = substr($seq,$i,80);
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57 print O "$subseq\n";
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58 }
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59 }
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60 close(O);
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