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added test for chlorodb

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Former-commit-id: 639cbbdc91a6c7f11544dbbe1fa0c47e1e28eaad
Former-commit-id: 59f6ff3f727d01f3ed4d553a554b322b24119b06
This commit is contained in:
alain viari
2015-11-13 18:53:47 +01:00
parent 13b03062d5
commit 42707c281c
17 changed files with 433 additions and 12 deletions
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37
detectors/cds/tools/chlorodb/subdb/go_subdb.sh
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@ -27,7 +27,7 @@ set Delta = 0.5
set Covmin = 30
set Pmax = 1e-6
set Idmin = 30
set Sizmin = 5
set Sizmin = 10
if ($#Argv > 0) then
set Delta = $Argv[1]; Shift
@ -91,14 +91,17 @@ set noms = `awk '{print $1}' $PatFile`
foreach nom ($noms)
set pat = `egrep "^$nom " $PatFile | awk '{print $2}'`
$AwkCmd -f $LIB_DIR/db.filter.pat.awk -v PAT="$pat" P_$$ > D_$$/$nom.fst
Report D_$$/$nom.fst "pattern_filter"
set n = `egrep '^>' D_$$/$nom.fst | wc -l`
Notify " pattern : $nom : $n"
Report D_$$/$nom.fst "pattern_filter"
if ($n <= $Sizmin) \rm -f D_$$/$nom.fst
if ($n < $Sizmin) \rm -f D_$$/$nom.fst
end
set ok = `ls D_$$ | wc -l`
if ($ok == 0) goto fin
if ($ok == 0) then
Warning "no entries found after pattern selection (increase Sizmin = $Sizmin)"
goto fin
endif
#
# select by length
@ -115,12 +118,14 @@ foreach f (D_$$/*.fst)
Report E_$$/$nom.fst "length_filter"
set n = `egrep '^>' E_$$/$nom.fst | wc -l`
Notify " length filter : $nom : $n"
if ($n <= $Sizmin) \rm -f E_$$/$nom.fst
if ($n < $Sizmin) \rm -f E_$$/$nom.fst
end
set ok = `ls E_$$ | wc -l`
if ($ok == 0) goto fin
if ($ok == 0) then
Warning "no entries found after length selection (increase Sizmin = $Sizmin)"
goto fin
endif
#
# select by similarity
@ -152,12 +157,15 @@ foreach f (E_$$/*.fst)
set n = `egrep '^>' F_$$/$nom.fst | wc -l`
Notify " blast filter : $nom : $n"
if ($n <= $Sizmin) \rm -f F_$$/$nom.fst
if ($n < $Sizmin) \rm -f F_$$/$nom.fst
end
set ok = `ls D_$$ | wc -l`
if ($ok == 0) goto fin
set ok = `ls F_$$ | wc -l`
if ($ok == 0) then
Warning "no entries found after similarity selection (increase Sizmin = $Sizmin)"
goto fin
endif
#
# annotations
@ -187,7 +195,14 @@ Notify "copy $n files to $OutDir"
#
fin:
Notify "output directory : $OutDir"
set n = `find $OutDir -name \*.fst -print | wc -l`
if ($n == 0) then
Warning "no entries found : removing $OutDir"
\rm -r $OutDir
else
Notify "output directory : $OutDir : $n entries"
endif
\rm -r ?_$$