diff --git a/README.md b/README.md index 2ce2c44..4fdc1a5 100644 --- a/README.md +++ b/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) diff --git a/cre.orphanet.sh b/cre.orphanet.sh index 772cd01..57667e0 100755 --- a/cre.orphanet.sh +++ b/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