From 14aae16a559268022d95bd6fa2d39da1dd87be75 Mon Sep 17 00:00:00 2001
From: Alexis CRISCUOLO <alexis.criscuolo@pasteur.fr>
Date: Sat, 4 Jan 2025 16:40:46 +0100
Subject: [PATCH] 0.5
---
forest.sh | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/forest.sh b/forest.sh
index 14ededd..8ae3397 100755
--- a/forest.sh
+++ b/forest.sh
@@ -299,7 +299,7 @@ dcheck() {
fi
## tac >8.0 ########################
echo -e -n "> \e[1mtac\e[0m >8.0 mandatory\t" ; binexe=$TAC_BIN;
- echo -e -n "$binexe \t\t" ;
+ echo -e -n "$binexe \t\t" ;
if [ ! $(command -v $binexe) ]; then echo -e "\e[31m[fail]\e[0m";
else echo -e -n "$(which $binexe)\t\t\e[32m[ok]\e[0m\t\t"; $TAC_BIN --version | sed -n '1p;q' ;
fi
@@ -543,7 +543,7 @@ then
# selecting trees
mv $FOREST $TMP ;
- while IFS=$'\t' read -r llk tre
+ while read -r llk tre # using IFS=$'\t' is slow...
do
chk=$($BAWK -v d=$DELTA '($1-$2<=d){print"OK"}' <<<"$BESTLK $llk");
[ "$chk" == "OK" ] && echo -e "$llk\t$tre" >> $FOREST ;
@@ -572,7 +572,7 @@ else ############################## <=== option -t
# checking no. sequences and leaves
na=$(grep "^>" $ALN | wc -l);
- while read t
+ while read -r t
do
nt=$(tr '(,' '\n' <<<"$t" | grep -c -v "^$");
if [ $nt -ne $na ]
@@ -598,7 +598,7 @@ else ############################## <=== option -t
tml="$(sed -n '1p;q' $MLTREE)";
hml="$(hashtree $tml)";
# discarding duplicate trees (if any)
- while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $MLTREE |
+ while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $MLTREE |
grep -v -F "$hml" |
sort |
$TAWK '($1==p){next} {p=$1;print$2}' > $TMP ;
@@ -643,7 +643,7 @@ else ############################## <=== option -t
# adding other trees
cat $TMP >> $INTREES ;
# discarding duplicate trees (if any) and the ML one
- while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $INTREES |
+ while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $INTREES |
grep -v -F "$hml" |
sort |
$TAWK '($1==p){next} {p=$1;print$2}' > $TMP ;
@@ -671,7 +671,7 @@ else ############################## <=== option -t
$BAWK '(NR==1){print$2}' $TMP> $MLTREE ;
# selecting trees
- while IFS=$'\t' read -r llk tre
+ while read -r llk tre # using IFS=$'\t' is slow...
do
chk=$($BAWK -v d=$DELTA '($1-$2<=d){print"OK"}' <<<"$BESTLK $llk");
[ "$chk" == "OK" ] && echo -e "$llk\t$tre" >> $FOREST ;
@@ -721,7 +721,7 @@ then
# building neighborhoods
cat $CURRENT | bash -c "$NEIGHBORHOOD" |
- while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP ;
+ while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP ;
# discarding already processed trees
cat $TMP $HASHSET |
@@ -834,7 +834,7 @@ then
# building neighborhoods
cat $CURRENT.$t | bash -c "$NEIGHBORHOOD" |
- while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP.$t &
+ while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP.$t &
t=$(( $t - 1 ));
done
--
GitLab