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2
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1 use strict;
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2
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3 my $fasta = $ARGV[0];
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4 my $phylip = $ARGV[1];
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5 my $out = $ARGV[2];
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6
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7 my @ids;
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8 open(F,$fasta) or die "Can not open file $fasta";
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9 while(<F>){
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10 if (/>(.*)/){
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11 my $id = $1;
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12 push(@ids,$id);
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13 }
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14 }
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15 close(F);
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16
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17 open(O,">$out") or die "Can not open and write into file $out";
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18 open(P,$phylip) or die "Can not open file $phylip";
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19 my $numline = 0;
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20 while(<P>){
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21 my $line = $_;
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22 $numline++;
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23 if (/^([\w\-]+)\s+/ && $numline > 1){
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24 my $reported_id = $1;
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25 my $id = $ids[$numline-2];
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26 $line =~s/$reported_id/$id/g;
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27 print O $line;
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28 }
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29 else{
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30 print O $line;
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31 }
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32 }
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33 close(P);
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34 close(O);
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