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Commit e095cb37 authored by Alexis CRISCUOLO's avatar Alexis CRISCUOLO :black_circle:
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1.1

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ASSU.sh
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......@@ -33,6 +33,8 @@
# #
VERSION=1.1; #
# + SSUdb inside a dedicated directory ($SSUDB_DIR) #
# + modified model sequence selection criterion #
# + updated verbose (option -v) #
# #
# VERSION=1.0; #
# #
......@@ -316,22 +318,14 @@ dcheck() {
# >> displays the content of the specified SSU databank #
# #
dispdb() {
# $ZGREP "^>" $1 |
# tr -d '>' |
# $BAWK ' {if($2=="A"){k="Archaea";++a}
# else {k="Bacteria";++b}
# if($3=="Candidatus")print k" | "$1" | "$3" "$4" "$5;
# else print k" | "$1" | "$3" "$4}
# END{print"# Archaea: "a;
# print"# Bacteria: "b}' ;
$GUNZIP -c $1 2>/dev/null |
tr -d '>' | paste - - | tr '\t' ' ' |
$BAWK ' {if($2=="A"){k="Archaea";++a}
else {k="Bacteria";++b}
if($3=="Candidatus")print k" | "$1" | "length($NF)" bps | "$3" "$4" "$5;
if($3=="Candidatus")print k" | "$1" | "length($NF)" bps | "$3" "$4" "$5;
else print k" | "$1" | "length($NF)" bps | "$3" "$4}
END{print"# Archaea: "a;
print"# Bacteria: "b}' ;
END{print"# Archaea: "a;
print"# Bacteria: "b}' ;
}
# #
##############################################################################################################
......@@ -524,7 +518,7 @@ then
case $fext in
fq|fastq) sed -n 2~4p $f | $BAWK '(FNR>10000){exit}{print length()}' ;;
gz) if $PZ ; then $PUNZIP -c -p $NTHREADS $f 2>/dev/null | sed -n 2~4p | $BAWK '(FNR>10000){exit}{print length()}' ;
else $GUNZIP -c $f 2>/dev/null | sed -n 2~4p | $BAWK '(FNR>10000){exit}{print length()}' ; fi ;;
else $GUNZIP -c $f 2>/dev/null | sed -n 2~4p | $BAWK '(FNR>10000){exit}{print length()}' ; fi ;;
bz|bz2) $BUNZIP -c $f 2>/dev/null | sed -n 2~4p | $BAWK '(FNR>10000){exit}{print length()}' ;;
dsrc|dsrc2) $DUNZIP $DSRCopt $f 2>/dev/null | sed -n 2~4p | $BAWK '(FNR>10000){exit}{print length()}' ;;
esac
......@@ -616,9 +610,9 @@ else
$ZGREP -E "$PATTERN" $SSUDB | $BAWK '{print$1}' | tr -d '>' > $TMP1 ;
# maximizing the sum of alignment scores (AS:i:) among the selected reference sequences
accn=$($TAWK '{print$3"\t"$14}' $SAM | sed 's/AS:i://g' |
$TAWK '{s[$1]+=$2}END{for(a in s)print s[a]"\t"a}' |
grep -F -f $TMP1 |
sort -rg | $TAWK '(NR==1){print$2;exit}');
$TAWK '{s[$1]+=$2}END{for(a in s)print s[a]"\t"a}' |
grep -F -f $TMP1 |
sort -rg | $TAWK '(NR==1){print$2;exit}');
fi
if [ -z "$accn" ]
......
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