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20
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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
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6 my $usage = qq~Usage:$0 <args> [<opts>]
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7 where <args> are:
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8 -i, --input <input VCF>
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9 -o, --output <output>
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10 -g, --gff <GFF annotation>
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11 -f, --fasta <Fasta of chromosomes>
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12 -h, --html <HTML output>
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13 ~;
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14 $usage .= "\n";
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15
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16 my ($input,$output,$gff,$fasta,$html);
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17
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18
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19 GetOptions(
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20 "input=s" => \$input,
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21 "output=s" => \$output,
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22 "gff=s" => \$gff,
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23 "fasta=s" => \$fasta,
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24 "html=s" => \$html
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25 );
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26
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27
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28 die $usage
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29 if ( !$input || !$output || !$fasta || !$gff || !$html);
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30
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31
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32 if (!-e $gff){
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33 die "Error: GFF input does not exist\n"
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34 }
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35 if (!-e $fasta){
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36 die "Error: Fasta input does not exist\n"
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37 }
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38
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39 my $SNPEFF_PATH = "/usr/local/bioinfo/galaxy/galaxy_dist/tools/SNiPlay/SnpEff/snpEff";
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40 #my $SNPEFF_PATH = $ENV{SNPEFF_JAR_PATH};
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41
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42
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43 my $session = $$;
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44 mkdir($session);
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45 mkdir("$session/data");
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46 mkdir("$session/data/genomes");
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47 mkdir("$session/data/myspecies");
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48
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49 system("cp -rf $fasta $session/data/genomes/myspecies.fa");
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50 system("cp -rf $gff $session/data/myspecies/genes.gff");
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51
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52 open(my $C,"$SNPEFF_PATH/snpEff.config");
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53 open(my $C2,">$session/snpEff.config");
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54 while(<$C>)
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55 {
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56 if (/data_dir/)
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57 {
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58 print $C2 "data_dir = ./data\n";
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59 }
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60 elsif (/^genomes/)
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61 {
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62 print $C2 "genomes : \\n";
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63 print $C2 "myspecies, myspecies \\n";
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64 }
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65 else
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66 {
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67 print $C2 $_;
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68 }
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69 }
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70 print $C2 "myspecies.genome : myspecies\n";
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71 close($C);
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72 close($C2);
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73
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74
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75 my $build_cmd = "/usr/local/jre/bin/java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies";
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76 system($build_cmd);
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77
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78 my $eff_cmd = "/usr/local/jre/bin/java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
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79 system($eff_cmd);
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80
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81
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82 system("rm -rf $session");
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