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removed need of R igraph from chlorodb/subdb

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Former-commit-id: 574aace9be5804d728a877110f5f475d61644f75
Former-commit-id: 2e7ea63447643830a62f18a364327d7b396ec140
This commit is contained in:
alain viari
2015-11-14 22:13:55 +01:00
parent d83201fd2f
commit 2d404b5b24
9 changed files with 81 additions and 66 deletions
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10
detectors/cds/tools/chlorodb/subdb/go_subdb.sh
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@ -111,9 +111,7 @@ Notify "select by length"
foreach f (D_$$/*.fst)
set nom = `basename $f:r`
$AwkCmd -f $LIB_DIR/db.getlen.awk $f > L_$$
$LIB_DIR/db.filter.len.r L_$$ $Delta |\
$AwkCmd '($NF == "TRUE") {print $2}' > M_$$
$AwkCmd -v DELTA=$Delta -f $LIB_DIR/db.filter.len.awk $f > M_$$
$AwkCmd -v FILE=M_$$ -f $LIB_DIR/db.subdb.awk $f > E_$$/$nom.fst
Report E_$$/$nom.fst "length_filter"
set n = `egrep '^>' E_$$/$nom.fst | wc -l`
@ -144,10 +142,8 @@ foreach f (E_$$/*.fst)
$AwkCmd -v COVMIN=$Covmin -v PMAX=$Pmax -v IDMIN=$Idmin \
-f $LIB_DIR/db.blastlink.awk $f.blast.out |\
$AwkCmd -f $LIB_DIR/db.todl.awk > G_$$
($LIB_DIR/db.cc.r G_$$ > $f.cc.txt) >>& db.log
$AwkCmd -f $LIB_DIR/db.cc.awk > $f.cc.txt
awk -v NAME=$nom -f $LIB_DIR/db.reportcc.awk $f.cc.txt >> $OutLog
$AwkCmd -f $LIB_DIR/db.selcc.awk $f.cc.txt > S_$$