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Commit b92e058d authored by Brandi Cantarel's avatar Brandi Cantarel
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remove biohpc hardcoded path

parent 91b0ea39
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......@@ -9,14 +9,14 @@ my ($genelist,$fpkm_file) = ("") x 2;
GetOptions( 'g|genes=s' => \$genelist,
'f|fpkm=s' => \$fpkm_file,
'i|refinfo=s'=> \$refinfo);
'i|geneinfo=s'=> \$refinfo);
my $fpkm_out = $fpkm_file;
$fpkm_out =~ s/\.fpkm.+txt/\.fpkm.capture.txt/;
open OUT, ">$fpkm_out" or die $!;
#gene_info.human.txt file is required for gene alias information
open GENEINFO, "<$refinfo/gene_info.human.txt" or die $!;
open GENEINFO, "<$geneinfo" or die $!;
my %geneinfo;
while(my $gline = <GENEINFO>){
chomp $gline;
......
......@@ -19,6 +19,7 @@ do
p) pair_id=$OPTARG;;
s) stranded=$OPTARG;;
f) filter=$OPTARG;;
i) ginfo=$OPTARG;;
h) usage;;
esac
done
......@@ -54,6 +55,6 @@ if [[ -f $filter ]]
then
cd ..
mv ${pair_id}.fpkm.txt ${prefix}.fpkm.ori.txt
perl ${baseDir}/fpkm_subset_panel.pl -f ${prefix}.fpkm.ori.txt -g $filter
perl ${baseDir}/fpkm_subset_panel.pl -f ${prefix}.fpkm.ori.txt -g $filter -i $ginfo
mv ${prefix}.fpkm.capture.txt ${pair_id}.fpkm.txt
fi
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