From fa07acf10d9d2803718cb88cf08f6aa677aa59eb Mon Sep 17 00:00:00 2001
From: jgugliel <julien.guglielmini@pasteur.fr>
Date: Mon, 28 Mar 2022 10:52:15 +0200
Subject: [PATCH] Removed evalue filtering because some self hits might have
higher e-values and the other filters seem to be enough.
---
wGRR | 7 ++++---
wGRR.awk | 15 +++++++++++++--
2 files changed, 17 insertions(+), 5 deletions(-)
diff --git a/wGRR b/wGRR
index 9d104f7..01e5f68 100755
--- a/wGRR
+++ b/wGRR
@@ -7,7 +7,7 @@ trap 'rm -rf "$tmp"' EXIT
export LC_ALL=C
SECONDS=0
-readonly VERSION=0.7
+readonly VERSION=0.8
bold=$(tput bold)
normal=$(tput sgr0)
@@ -21,8 +21,9 @@ display_usage() {
echo "${bold}MANDATORY PARAMETERS:${normal}"
echo " -i <string> fasta file with all proteins of all the compared genetic elements."
echo " All identifiers must be formatted as:"
- echo " >element_identifier_XXX"
- echo " where XXX is a serie of numbers unique for each protein of each element."
+ echo " >elementId_XXX"
+ echo " where elementID is a string unique for each genetic element"
+ echo " and XXX is a serie of characters unique for each protein of each element."
echo "${bold}OPTIONS:${normal}"
echo " -p <string> Path to the mmseqs executable."
echo " e.g. /usr/local/bin"
diff --git a/wGRR.awk b/wGRR.awk
index 52bec67..94c0c71 100755
--- a/wGRR.awk
+++ b/wGRR.awk
@@ -66,7 +66,7 @@ FILENAME==ARGV[3] {
cov1=$3
cov2=$4
fid=$5
- evalue=$6
+# evalue=$6
bits=$7
# Fix for some evalues below awk precision
@@ -77,7 +77,8 @@ FILENAME==ARGV[3] {
}
}
- if(cov1<=COV || cov2<=COV || fid<=ID || evalue>=EVAL){
+# if(cov1<=COV || cov2<=COV || fid<=ID || evalue>=EVAL){
+ if(cov1<=COV || cov2<=COV || fid<=ID){
next
}
@@ -265,6 +266,16 @@ END {
lcj=lj_singleton+length(cluster)
lci<lcj ? lc=lci : lc=lcj
+ if(mp==0){
+ print "bad mp for genomes "gi" "gj
+ }
+ if(minprot==0){
+ print "bad minprot for genomes"gi" "gj
+ }
+ if(lc==0){
+ print "bad lc for genomes "gi" "gj
+ }
+
if(gi==gj){
lc = length(cluster)
if(!MEM){
--
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