Commit b5ede9a6 authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Remove unused file

parent bf9488e8
#!/usr/bin/make -f
# Makefile for running the INF pipeline
# Author: Marco Chierici <chierici@fbk.eu>
# Date: 2017-05-12
#
.PHONY: init
SHELL := /bin/bash
# input variables
# shown are examples, override on command line
FILE ?= data/AG1-G_MAV-G_498_LIT_ALL_tr.txt
LABEL ?= data/label_498_ALL-EFS_tr.lab
DATA1 ?= data/AG1-G_498_LIT_ALL_tr.txt
DATA2 ?= data/MAV-G_498_LIT_ALL_tr.txt
ENDPOINT ?= ALL-EFS
# added MF 20170710
THREADS ?= 4
OUTBASE ?= /path/to/out_tmp
BINDIR := .
OUTDIR := $(OUTBASE)/$(ENDPOINT)
# derived variables
OUTPREFIX = $(notdir $(basename $(FILE)))
LEVEL1 = $(word 1,$(subst _, ,$(OUTPREFIX)))
LEVEL2 = $(word 2,$(subst _, ,$(OUTPREFIX)))
init:
@mkdir -p $(OUTDIR)/rSNFi
@mkdir -p $(OUTDIR)/rSNF
all: init $(OUTDIR)/rSNFi/$(OUTPREFIX)_MCC_scores.txt $(OUTDIR)/rSNF/$(OUTPREFIX)_MCC_scores.txt $(OUTDIR)/juxt/$(OUTPREFIX)_MCC_scores.txt
$(OUTDIR)/juxt/$(OUTPREFIX)_RandomForest_KBest.log: $(FILE) $(LABEL)
python $(BINDIR)/sklearn_rf_training_fixrank.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/juxt --ranking KBest
$(OUTDIR)/juxt/$(OUTPREFIX)_MCC_scores.txt: $(OUTDIR)/juxt/$(OUTPREFIX)_RandomForest_KBest.log $(subst _tr,_ts,$(FILE)) $(subst _tr,_ts,$(LABEL))
python $(BINDIR)/sklearn_rf_validation_writeperf.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/juxt --tslab $(word 3,$^)
$(OUTDIR)/rSNF/INF_$(OUTPREFIX).txt: $(DATA1) $(DATA2) $(LABEL)
Rscript $(BINDIR)/snf_integration.R --d1 $(word 1,$^) --d2 $(word 2,$^) --lab $(word 3,$^) \
--scriptDir $(BINDIR)/SNFtools/ --clust spectral --threads "$(THREADS)" \
--outf $@
$(OUTDIR)/rSNF/$(OUTPREFIX)_RandomForest_rankList.log: $(FILE) $(LABEL) $(OUTDIR)/rSNF/INF_$(OUTPREFIX).txt
python $(BINDIR)/sklearn_rf_training_fixrank.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNF \
--ranking rankList --rankFeats $(word 3,$^)
$(OUTDIR)/rSNF/$(OUTPREFIX)_MCC_scores.txt: $(OUTDIR)/rSNF/$(OUTPREFIX)_RandomForest_rankList.log $(subst _tr,_ts,$(FILE)) $(subst _tr,_ts,$(LABEL))
python $(BINDIR)/sklearn_rf_validation_writeperf.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNF --tslab $(word 3,$^)
$(OUTDIR)/rSNFi/intersection_$(OUTPREFIX).txt: $(OUTDIR)/juxt/$(OUTPREFIX)_RandomForest_KBest.log $(OUTDIR)/rSNF/$(OUTPREFIX)_RandomForest_rankList.log
python $(BINDIR)/intersect_biomarkers.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNFi/venn_$(OUTPREFIX).png $@ --title1 "$(LEVEL1)" --title2 "$(LEVEL2)"
$(OUTDIR)/rSNFi/$(OUTPREFIX).txt: $(FILE) $(OUTDIR)/rSNFi/intersection_$(OUTPREFIX).txt
python $(BINDIR)/extract_topfeats_onecol.py $(word 1,$^) $(word 2,$^) $@
$(OUTDIR)/rSNFi/$(OUTPREFIX)_RandomForest_KBest.log: $(OUTDIR)/rSNFi/$(OUTPREFIX).txt $(LABEL)
python $(BINDIR)/sklearn_rf_training_fixrank.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNFi --ranking KBest
$(OUTDIR)/rSNFi/$(OUTPREFIX)_MCC_scores.txt: $(OUTDIR)/rSNFi/$(OUTPREFIX)_RandomForest_KBest.log $(subst _tr,_ts,$(FILE)) $(subst _tr,_ts,$(LABEL))
python $(BINDIR)/sklearn_rf_validation_writeperf.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNFi --tslab $(word 3,$^)
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