Commit 3d0b2086 authored by Carine Rey's avatar Carine Rey
Browse files

fix error with HaPC*Ne

parent 5fc3531f
...@@ -71,11 +71,10 @@ let bppseqgen_multi_profiles_script ~config ~out ~profile_c = ...@@ -71,11 +71,10 @@ let bppseqgen_multi_profiles_script ~config ~out ~profile_c =
i=0 i=0
while read -r line while read -r line
do do
echo "i: $i"
((i++)) ((i++))
name="$line"
COL_M1=`echo $line | cut -f 1 -d " "` COL_M1=`echo $line | cut -f 1 -d " "`
COL_M2=`echo $line | cut -f 2 -d " "` COL_M2=`echo $line | cut -f 2 -d " "`
echo "i: $i" "COL_M1: $COL_M1" "COL_M2: $COL_M2"
bppseqgen param=$PARAM i=$i COL_M1=$COL_M1 COL_M2=$COL_M2 output.sequence.file=out_int_"$i".fa bppseqgen param=$PARAM i=$i COL_M1=$COL_M1 COL_M2=$COL_M2 output.sequence.file=out_int_"$i".fa
done < "$PROFILE_C" done < "$PROFILE_C"
......
...@@ -76,7 +76,7 @@ let bpp_config_HaPCOC_F_Ne = seq ~sep:"\n" [ ...@@ -76,7 +76,7 @@ let bpp_config_HaPCOC_F_Ne = seq ~sep:"\n" [
let bpp_config_HaPC_F_Ne = seq ~sep:"\n" [ let bpp_config_HaPC_F_Ne = seq ~sep:"\n" [
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ; seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ;
seq [string "modelT=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ; seq [string "modelT=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)), Ns=$(NE_T))" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)), Ns=$(NE_C))" ] ; seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)), Ns=$(NE_C))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ; seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
] ]
......
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