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Commit a6cbfc92 authored by Alessia Marcolini's avatar Alessia Marcolini
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Remove ancient flags

parent dbc4e4fb
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Snakefile_full
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......@@ -131,7 +131,7 @@ rule ml_juxt_tr:
rule ml_juxt_val:
input:
ancient("{outfolder}/{dataset}/{target}/{model}/{split_id}/juxt/{layers}_tr_{model}_KBest.log"),
"{outfolder}/{dataset}/{target}/{model}/{split_id}/juxt/{layers}_tr_{model}_KBest.log",
os.path.join(DATAFOLDER, "{dataset}/{target}/{split_id}/{layers}_tr.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/{split_id}/{layers}_ts.txt"),
os.path.join(DATAFOLDER, "{dataset}/{target}/{split_id}/labels_{target}_ts.txt")
......@@ -142,10 +142,10 @@ rule ml_juxt_val:
rule snf:
input:
ancient(expand("{datafolder}/{dataset}/{target}/{split_id}/{layer}_tr_{{cv_n}}_{{cv_k}}.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layer=LAYERS, split_id=SPLIT_ID)),
ancient(expand("{datafolder}/{dataset}/{target}/{split_id}/labels_{target}_tr_{{cv_n}}_{{cv_k}}.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, split_id=SPLIT_ID)),
expand("{datafolder}/{dataset}/{target}/{split_id}/{layer}_tr_{{cv_n}}_{{cv_k}}.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layer=LAYERS, split_id=SPLIT_ID),
expand("{datafolder}/{dataset}/{target}/{split_id}/labels_{target}_tr_{{cv_n}}_{{cv_k}}.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, split_id=SPLIT_ID),
threads: 8
output:
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/INF_{layers}_tr_{{cv_n}}_{{cv_k}}.txt",
......@@ -161,12 +161,12 @@ rule snf:
rule ml_rsnf_tr:
input:
ancient(expand("{datafolder}/{dataset}/{target}/{split_id}/{layers}_tr.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID)),
ancient(expand("{datafolder}/{dataset}/{target}/{split_id}/labels_{target}_tr.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, split_id=SPLIT_ID)),
snf_rankings = ancient(expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/INF_{layers}_tr_{cv_n}_{cv_k}.txt",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, split_id=SPLIT_ID, layers=LAYERS_CONCAT, cv_n=list(range(CV_N)), cv_k=list(range(CV_K))))
expand("{datafolder}/{dataset}/{target}/{split_id}/{layers}_tr.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID),
expand("{datafolder}/{dataset}/{target}/{split_id}/labels_{target}_tr.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, split_id=SPLIT_ID),
snf_rankings = expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/INF_{layers}_tr_{cv_n}_{cv_k}.txt",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, split_id=SPLIT_ID, layers=LAYERS_CONCAT, cv_n=list(range(CV_N)), cv_k=list(range(CV_K)))
output:
"{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/{layers}_tr_{model}_rankList.log",
shell:
......@@ -175,12 +175,12 @@ rule ml_rsnf_tr:
rule ml_rsnf_val:
input:
ancient(expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/{layers}_tr_{model}_rankList.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID)),
ancient(expand("{datafolder}/{dataset}/{target}/{split_id}/{layers}_ts.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID)),
ancient(expand("{datafolder}/{dataset}/{target}/{split_id}/labels_{target}_ts.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID)),
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/{layers}_tr_{model}_rankList.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID),
expand("{datafolder}/{dataset}/{target}/{split_id}/{layers}_ts.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID),
expand("{datafolder}/{dataset}/{target}/{split_id}/labels_{target}_ts.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID),
output:
"{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/{layers}_tr_MCC_scores.txt",
shell:
......@@ -189,10 +189,10 @@ rule ml_rsnf_val:
rule myintersect:
input:
ancient(expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/juxt/{layers}_tr_{model}_KBest.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID)),
ancient(expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/{layers}_tr_{model}_rankList.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID))
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/juxt/{layers}_tr_{model}_KBest.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID),
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNF/{layers}_tr_{model}_rankList.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID)
output:
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNFi/{layers}_intersect_tr.txt",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID)
......@@ -202,10 +202,10 @@ rule myintersect:
rule extract:
input:
ancient(expand("{datafolder}/{dataset}/{target}/{split_id}/{layers}_ts.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID)),
ancient(expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNFi/{layers}_intersect_tr.txt",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID))
expand("{datafolder}/{dataset}/{target}/{split_id}/{layers}_ts.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, layers=LAYERS_CONCAT, split_id=SPLIT_ID),
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNFi/{layers}_intersect_tr.txt",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID)
output:
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNFi/{layers}_ts.txt",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, layers=LAYERS_CONCAT, split_id=SPLIT_ID)
......@@ -227,8 +227,8 @@ rule ml_rsnfi_tr:
rule ml_rsnfi_val:
input:
ancient(expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNFi/{layers}_ts_{model}_KBest.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, split_id=SPLIT_ID, layers=LAYERS_CONCAT)),
expand("{outfolder}/{dataset}/{target}/{model}/{split_id}/rSNFi/{layers}_ts_{model}_KBest.log",
outfolder=OUTFOLDER, dataset=DATASET, target=TARGET, model=MODEL, split_id=SPLIT_ID, layers=LAYERS_CONCAT),
expand("{datafolder}/{dataset}/{target}/{split_id}/{layers}_ts2.txt",
datafolder=DATAFOLDER, dataset=DATASET, target=TARGET, split_id=SPLIT_ID, layers=LAYERS_CONCAT),
expand("{datafolder}/{dataset}/{target}/{split_id}/labels_{target}_ts2.txt",
......
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