Mercurial > repos > dereeper > sniplay3
diff snpEff/SnpEff.pl @ 23:a1ab979f4551 draft
Uploaded
| author | dereeper |
|---|---|
| date | Mon, 23 Mar 2015 05:52:17 -0400 |
| parents | 13cff72ec2d3 |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff/SnpEff.pl Mon Mar 23 05:52:17 2015 -0400 @@ -0,0 +1,82 @@ +#!/usr/bin/perl + +use strict; +use Getopt::Long; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --input <input VCF> + -o, --output <output> + -g, --gff <GFF annotation> + -f, --fasta <Fasta of chromosomes> + -h, --html <HTML output> +~; +$usage .= "\n"; + +my ($input,$output,$gff,$fasta,$html); + + +GetOptions( + "input=s" => \$input, + "output=s" => \$output, + "gff=s" => \$gff, + "fasta=s" => \$fasta, + "html=s" => \$html +); + + +die $usage + if ( !$input || !$output || !$fasta || !$gff || !$html); + + +if (!-e $gff){ + die "Error: GFF input does not exist\n" +} +if (!-e $fasta){ + die "Error: Fasta input does not exist\n" +} + +#my $SNPEFF_PATH = "/usr/local/bioinfo/galaxy/galaxy_dist/tools/SNiPlay/SnpEff/snpEff"; +my $SNPEFF_PATH = $ENV{SNPEFF_JAR_PATH}; + + +my $session = $$; +mkdir($session); +mkdir("$session/data"); +mkdir("$session/data/genomes"); +mkdir("$session/data/myspecies"); + +system("cp -rf $fasta $session/data/genomes/myspecies.fa"); +system("cp -rf $gff $session/data/myspecies/genes.gff"); + +open(my $C,"$SNPEFF_PATH/snpEff.config"); +open(my $C2,">$session/snpEff.config"); +while(<$C>) +{ + if (/data_dir/) + { + print $C2 "data_dir = ./data\n"; + } + elsif (/^genomes/) + { + print $C2 "genomes : \\n"; + print $C2 "myspecies, myspecies \\n"; + } + else + { + print $C2 $_; + } +} +print $C2 "myspecies.genome : myspecies\n"; +close($C); +close($C2); + + +my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies"; +system($build_cmd); + +my $eff_cmd = "java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output"; +system($eff_cmd); + + +system("rm -rf $session");