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MPBA
INF
Commits
b5ede9a6
Commit
b5ede9a6
authored
Mar 26, 2020
by
Alessia Marcolini
Browse files
Remove unused file
parent
bf9488e8
Changes
1
Hide whitespace changes
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Side-by-side
Makefile
deleted
100755 → 0
View file @
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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