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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 use Getopt::Long;
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5 use Bio::SeqIO;
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6 use File::Basename;
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7 my $dirname = dirname(__FILE__);
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8 use Cwd qw(cwd);
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9 my $dir = cwd;
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10
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11 my $usage = qq~Usage:$0 <args> [<opts>]
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12
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13 where <args> are:
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14
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15 -g, --genes <list of gene fasta files. Comma separated list>
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16 -p, --proteins <list of protein fasta files. Comma separated list>
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2
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17 -l, --list <list of samples in the same order. Comma separated list>
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18 -o, --out <output name>
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19 ~;
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20 $usage .= "\n";
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21
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22 my ($genes,$proteins,$out,$order);
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23
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24 GetOptions(
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25 "genes=s" => \$genes,
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26 "proteins=s" => \$proteins,
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27 "out=s" => \$out,
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2
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28 "list=s" => \$order
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29 );
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30
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31
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32 die $usage
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33 if ( !$proteins || !$genes || !$out || !$order);
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34
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5
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35 if ($order =~/^,(.*)$/){
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36 $order = $1;
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37 }
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0
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38 my @names = split(",",$order);
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39 mkdir("tmpdir$$");
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40 my @gene_files = split(/,/,$genes);
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41 my $n = 0;
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42 foreach my $gene_file(@gene_files){
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1
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43 my $particule = $names[$n];
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44 system("cp $gene_file tmpdir$$/$particule.nuc");
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45 $n++;
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46 }
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47 $n = 0;
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48 my @protein_files = split(/,/,$proteins);
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49 foreach my $protein_file(@protein_files){
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5
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50 my $particule = $names[$n];
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51 system("cp $protein_file tmpdir$$/$particule.pep");
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52 open(F,"$protein_file");
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53 open(F2,">tmpdir$$/$particule.function");
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54 while(<F>){
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55 if (/>(.*)/){
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56 print F2 "$1 - unknown\n";
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57 }
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58 }
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59 close(F);
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60 close(F2);
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61 $n++;
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62 }
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63
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64 #chdir("$dirname/PGAP-1.2.1");
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5
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65 my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@names)." --method GF";
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66 system($cmd);
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67 system("cp -rf outdir/1.Orthologs_Cluster.txt $out");
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