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