From 2a4e29ab7ca1f0d24848ab38f0dc566792b24947 Mon Sep 17 00:00:00 2001 From: Stephen Ficklin Date: Thu, 20 Jun 2019 18:30:41 -0700 Subject: [PATCH] Update KEGG.sh --- terms/KEGG.sh | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/terms/KEGG.sh b/terms/KEGG.sh index b65e642..9275349 100644 --- a/terms/KEGG.sh +++ b/terms/KEGG.sh @@ -1,12 +1,12 @@ -lynx "http://www.genome.jp/kegg-bin/download_htext?htext=ko00001.keg&format=htext&filedir=" +wget "http://www.genome.jp/kegg-bin/download_htext?htext=ko00001.keg&format=htext&filedir=" -O ko00001.keg # first get the list of pathways -grep -P "^C" ko00001.keg > pathways.txt -perl -pi -e 's/^C\s+(\d+)\s(.*?)\s*\[.*/KEGG\tko\1\t\2/' pathways.txt +grep -P "^C" ko00001.keg | grep "\[PATH:" | \ +perl -p -e 's/^C\s+(\d+)\s(.*?)\s*\[PATH:(.*)\].*/KEGG\t\3\t\2/' > pathways.txt # second get the list of othologs -egrep "K0|K1" ko00001.keg > orthologs.txt -perl -pi -e 's/^D\s+(K\d+)\s+.*?;\s+(.*?)/KEGG\t\1\t\2/' orthologs.txt +grep -P "^D" ko00001.keg | \ +perl -p -e 's/^D\s+(K\d+)\s+.*?;\s+(.*?)/KEGG\t\1\t\2/' > orthologs.txt cat pathways.txt orthologs.txt > KEGG.terms.txt