Commit 7ccd4647 authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Fix dataset folder

parent cd000267
......@@ -21,8 +21,8 @@ rule all:
rule ml_juxt_tr:
input:
os.path.join(DATAFOLDER, "{dataset}/{layer1}_{layer2}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_tr.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer1}_{layer2}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_tr.txt")
output:
"{outfolder}/{dataset}/{target}/juxt/{layer1}_{layer2}_tr_RandomForest_KBest.log"
shell:
......@@ -32,8 +32,8 @@ rule ml_juxt_tr:
rule ml_juxt_val:
input:
"{outfolder}/{dataset}/{target}/juxt/{layer1}_{layer2}_tr_RandomForest_KBest.log",
os.path.join(DATAFOLDER, "{dataset}/{layer1}_{layer2}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_ts.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer1}_{layer2}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_ts.txt")
output:
"{outfolder}/{dataset}/{target}/juxt/{layer1}_{layer2}_tr_MCC_scores.txt"
shell:
......@@ -41,9 +41,9 @@ rule ml_juxt_val:
rule snf:
input:
os.path.join(DATAFOLDER, "{dataset}/{layer1}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{layer2}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_tr.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer1}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}//{layer2}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}//labels_{target}_tr.txt")
threads: 8
output:
"{outfolder}/{dataset}/{target}/rSNF/INF_{layer1}_{layer2}_tr.txt"
......@@ -55,8 +55,8 @@ rule snf:
rule ml_rsnf_tr:
input:
os.path.join(DATAFOLDER, "{dataset}/{layer1}_{layer2}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer1}_{layer2}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_tr.txt"),
"{outfolder}/{dataset}/{target}/rSNF/INF_{layer1}_{layer2}_tr.txt"
output:
"{outfolder}/{dataset}/{target}/rSNF/{layer1}_{layer2}_tr_RandomForest_rankList.log"
......@@ -67,8 +67,8 @@ rule ml_rsnf_tr:
rule ml_rsnf_val:
input:
"{outfolder}/{dataset}/{target}/rSNF/{layer1}_{layer2}_tr_RandomForest_rankList.log",
os.path.join(DATAFOLDER, "{dataset}/{layer1}_{layer2}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_ts.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer1}_{layer2}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_ts.txt")
output:
"{outfolder}/{dataset}/{target}/rSNF/{layer1}_{layer2}_tr_MCC_scores.txt"
shell:
......@@ -87,7 +87,7 @@ rule myintersect:
rule extract:
input:
os.path.join(DATAFOLDER, "{dataset}/{layer1}_{layer2}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer1}_{layer2}_tr.txt"),
"{outfolder}/{dataset}/{target}/rSNFi/{layer1}_{layer2}_intersect_tr.txt"
output:
"{outfolder}/{dataset}/{target}/rSNFi/{layer1}_{layer2}_tr.txt"
......@@ -98,7 +98,7 @@ rule extract:
rule ml_rsnfi_tr:
input:
"{outfolder}/{dataset}/{target}/rSNFi/{layer1}_{layer2}_tr.txt",
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_tr.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_tr.txt")
output:
"{outfolder}/{dataset}/{target}/rSNFi/{layer1}_{layer2}_tr_RandomForest_KBest.log"
shell:
......@@ -108,8 +108,8 @@ rule ml_rsnfi_tr:
rule ml_rsnfi_val:
input:
"{outfolder}/{dataset}/{target}/rSNFi/{layer1}_{layer2}_tr_RandomForest_KBest.log",
os.path.join(DATAFOLDER, "{dataset}/{layer1}_{layer2}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_ts.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer1}_{layer2}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_ts.txt")
output:
"{outfolder}/{dataset}/{target}/rSNFi/{layer1}_{layer2}_tr_MCC_scores.txt"
shell:
......@@ -118,8 +118,8 @@ rule ml_rsnfi_val:
rule single_tr:
input:
os.path.join(DATAFOLDER, "{dataset}/{layer}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_tr.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_tr.txt")
output:
"{outfolder}/{dataset}/{target}/single/{layer}_tr_RandomForest_KBest.log"
shell:
......@@ -128,8 +128,8 @@ rule single_tr:
rule single_val:
input:
"{outfolder}/{dataset}/{target}/single/{layer}_tr_RandomForest_KBest.log",
os.path.join(DATAFOLDER, "{dataset}/{layer}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/labels_{target}_ts.txt")
os.path.join(DATAFOLDER, "{dataset}/{target}/{layer}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/labels_{target}_ts.txt")
output:
"{outfolder}/{dataset}/{target}/single/{layer}_tr_MCC_scores.txt"
shell:
......
......@@ -3,11 +3,12 @@
THREADS=12
OUTFOLDER=results_breast
DATAFOLDER=data/breast
OUTFOLDER=results
DATAFOLDER=data
DATASET=tcga_breast
LAYER1=gene
LAYER2=cnv
TARGET=ER
# go!
snakemake --cores $THREADS --config datafolder=$DATAFOLDER outfolder=$OUTFOLDER target=$TARGET layer1=$LAYER1 layer2=$LAYER2
snakemake --cores $THREADS --config datafolder=$DATAFOLDER outfolder=$OUTFOLDER dataset=$DATASET target=$TARGET layer1=$LAYER1 layer2=$LAYER2 -p
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