modified: README.md

	modified:   cre.orphanet.sh

README.md

@@ -28,8 +28,7 @@ Excel variant report generator and scripts to process WES data (cram/bam/fastq -
   5. (Optional) Install/update Orphanet.
 ```
     cd ~/cre/data
-    wget http://www.orphadata.org/data/xml/en_product6.xml
-    cre.orphanet.sh
+    ~/cre/cre.orphanet.sh
 ```
   Orphanet provides descriptions for ~3600 genes:. By default CRE uses [orphanet.txt](../master/data/orphanet.txt)
 

cre.orphanet.sh

@@ -25,6 +25,4 @@ cat en_product6.xml.final | awk '{if($0 ~ "ENSG") {print $0"\t"dis}else{dis=$0}}
 cat orphanet.tmp | sort -k1,1 > orphanet.sorted.txt
 cat orphanet.sorted.txt  | awk -F "\t" 'BEGIN{prev_gene="Ensembl_gene_id\tOrphanet";buf=""}{if(prev_gene != $1){print prev_gene"\t"buf;buf=$2;prev_gene=$1}else{buf=buf","$2;}}END{print prev_gene","buf'} > orphanet.txt
 
-cp orphanet.txt ~/cre
-
 rm en_product6.* orphanet.tmp orphanet.sorted.txt