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Commit ed65bfda authored by ysard's avatar ysard
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Split Cadbiom project to 3 dependent packages

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.gitignore
View file @ ed65bfda
*.o
MANIFEST
*.egg-info
*dist/
*build/
files.txt
*.pyc
.*.swp
.*.swo
......
Makefile deleted 100644 → 0
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CMD_PYTHON=python
PYTHON=$(CMD_PYTHON) -m cadbiom
#LOGLEVEL=--loglevel=debug
#LOGLEVEL=--loglevel=info
COMMAND=$(PYTHON) $(LOGLEVEL)
.PHONY: all
all: build
.PHONY: build
build:
pip install -r requirements.txt
.PHONY: run_gui
run_gui:
@echo Launch GUI
$(COMMAND) run_gui
unit_test:
@echo Unit tests...
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/mini_test_publi.bcx Px --steps 10
py.test
@# cluster unit tests
@#../.local/bin/py.test test
multiprocess:
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/pid_and_clock.bcx --input_file bio_models/input.txt --steps 7 --output run
t1:
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/pid_and_clock.bcx SRP9 --steps 10 --output p1
t2:
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/pid_and_clock.bcx SRP9 --steps 7 --output p2
t3:
$(CMD_PYTHON) cadbiom_cmd.py -vv info compute_macs "bio_models/Whole NCI-PID database translated into CADBIOM formalism(and).bcx" SRP9 --all_macs --steps 10 --output bench
t3bis:
$(CMD_PYTHON) cadbiom_cmd.py -vv info compute_macs "bio_models/Whole NCI-PID database translated into CADBIOM formalism(and).bcx" SRP9 --steps 10 --output p3bis
t4:
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/pid_or_clock.bcx SRP9 --steps 7 --output p4
t5:
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/pid_and_clock.bcx CCR5 --steps 10 --output p5
t6:
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/pid_and_clock.bcx CCR5 --steps 7 --output p6
t7:
$(CMD_PYTHON) cadbiom_cmd.py -vv debug compute_macs bio_models/pid_or_clock.bcx CCR5 --steps 7 --output p7
real_study:
$(CMD_PYTHON) cadbiom_cmd.py -vv info compute_macs "bio_models/Whole NCI-PID database translated into CADBIOM formalism(and).bcx" --steps 7 --all_macs --input_file bio_models/input_places.txt --combinations
version:
$(COMMAND) --version
_cadbiom/MANIFEST deleted 100644 → 0
View file @ 44ce61b5
# file GENERATED by distutils, do NOT edit
setup.py
src/cadbiom.c
bio_models/input_places.txt deleted 100644 → 0
View file @ 44ce61b5
TGFB1
COL1A1
decorin
MMP2
MMP9
TIMP1
bio_models/mini_test_publi.bcx deleted 100644 → 0
View file @ 44ce61b5
<model xmlns="http://cadbiom" name="bicluster">
<CSimpleNode name="Ax" xloc="0.156748911466" yloc="0.673568818514"/>
<CSimpleNode name="n1" xloc="0.291727140784" yloc="0.673568818514"/>
<CSimpleNode name="C1" xloc="0.404208998548" yloc="0.618757612668"/>
<CSimpleNode name="n2" xloc="0.405660377359" yloc="0.722289890377"/>
<CSimpleNode name="Px" xloc="0.577083086261" yloc="0.722140333368"/>
<CSimpleNode name="Bx" xloc="0.157474600871" yloc="0.83922046285"/>
<CSimpleNode name="n3" xloc="0.290570367401" yloc="0.803822907245"/>
<CSimpleNode name="n4" xloc="0.292715433748" yloc="0.906099768906"/>
<CSimpleNode name="C2" xloc="0.409124108889" yloc="0.803710739487"/>
<CSimpleNode name="C3" xloc="0.408336298212" yloc="0.906099768906"/>
<transition name="" ori="Ax" ext="n1" event="h00" condition="" action="" fact_ids="[]"/>
<transition name="" ori="n1" ext="C1" event="h0" condition="" action="" fact_ids="[]"/>
<transition name="" ori="n1" ext="n2" event="h1" condition="C2" action="" fact_ids="[]"/>
<transition name="" ori="n2" ext="Px" event="hlast" condition="C1 and not C3" action="" fact_ids="[]"/>
<transition name="" ori="Bx" ext="n3" event="h2" condition="" action="" fact_ids="[]"/>
<transition name="" ori="Bx" ext="n4" event="h4" condition="" action="" fact_ids="[]"/>
<transition name="" ori="n3" ext="C2" event="h3" condition="" action="" fact_ids="[]"/>
<transition name="" ori="n4" ext="C3" event="h5" condition="" action="" fact_ids="[]"/>
</model>
bio_models/pid_and_clock.bcx deleted 100644 → 0
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bio_models/pid_or_clock.bcx deleted 100644 → 0
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bio_models/solution/p21reachable_tgfCanonical.graphml deleted 100644 → 0
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bio_models/solution/p21reachable_tgfCanonical.txt deleted 100644 → 0
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SP1 betaglycan__dimer___intToMb TRAP_1_TGFBR1__dimer___inactive_intToMb importinalpha NUP153 TGFBfamily__dimer___active_exCellRegion GCN5 NUP214 TGFBR2__dimer___active_intToMb Axin_SMAD3 SMAD4_cy CTGF
% _h_12
% _h_10
% _h_16
% _h_11 _h_43
% _h_40 _h_45
% _h_64
% _h_57
% _h_80
SP1 betaglycan__dimer___intToMb TRAP_1_TGFBR1__dimer___inactive_intToMb importinalpha importinbeta TGFBfamily__dimer___active_exCellRegion GCN5 TGFBR2__dimer___active_intToMb Axin_SMAD3 SMAD4_cy CTGF
% _h_12
% _h_10
% _h_16
% _h_11 _h_43
% _h_40 _h_45
% _h_64
% _h_57
% _h_80
SP1 betaglycan__dimer___intToMb importinalpha NUP153 TGFBfamily__dimer___active_exCellRegion NUP214 TGFBR2__dimer___active_intToMb Axin_SMAD3 SMAD4_cy Cbp_p300_MSG1_nucl FKBP12_TGFBR1__dimer___inactive_intToMb CTGF
% _h_12
% _h_19
% _h_16
% _h_43
% _h_40
% _h_64
% _h_57
% _h_80
SP1 betaglycan__dimer___intToMb TRAP_1_TGFBR1__dimer___inactive_intToMb PCAF_nucl importinalpha NUP153 TGFBfamily__dimer___active_exCellRegion NUP214 TGFBR2__dimer___active_intToMb Axin_SMAD3 SMAD4_cy Cbp_p300_nucl CTGF
% _h_12
% _h_10
% _h_16
% _h_11 _h_43
% _h_40 _h_45
% _h_64
% _h_57
% _h_80
SP1 betaglycan__dimer___intToMb TRAP_1_TGFBR1__dimer___inactive_intToMb importinalpha NUP153 TGFBfamily__dimer___active_exCellRegion NUP214 Cbp_p300_PIAS3 TGFBR2__dimer___active_intToMb Axin_SMAD3 SMAD4_cy CTGF
% _h_12
% _h_10
% _h_16
% _h_11 _h_43
% _h_40 _h_45
% _h_64
% _h_57
% _h_80
SP1 betaglycan__dimer___intToMb TRAP_1_TGFBR1__dimer___inactive_intToMb importinalpha NUP153 TGFBfamily__dimer___active_exCellRegion NUP214 TGFBR2__dimer___active_intToMb Axin_SMAD3 SMAD4_cy Cbp_p300_MSG1_nucl CTGF
% _h_12
% _h_10
% _h_16
% _h_11 _h_43
% _h_40 _h_45
% _h_64
% _h_57
% _h_80
SP1 betaglycan__dimer___intToMb TRAP_1_TGFBR1__dimer___inactive_intToMb PCAF_nucl importinalpha importinbeta TGFBfamily__dimer___active_exCellRegion TGFBR2__dimer___active_intToMb Axin_SMAD3 SMAD4_cy Cbp_p300_nucl CTGF
% _h_12
% _h_10
% _h_16
% _h_11 _h_43
% _h_40 _h_45
% _h_64
% _h_57