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Updates to datasets II code #7

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greglandrum Aug 12, 2017
f0763b2
get most everything working with python3
greglandrum Oct 10, 2017
4029f33
add reversible (Crude!)
greglandrum Oct 10, 2017
84d67e7
update
greglandrum Nov 26, 2022
cef81bf
seems to work
greglandrum Nov 30, 2022
23e826d
additional validation funcs
greglandrum Nov 30, 2022
a1225b0
add BRF scorer
greglandrum Dec 18, 2022
7f6df3c
update NB scorer
greglandrum Dec 18, 2022
59fd09b
basics
greglandrum Dec 19, 2022
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28 changes: 14 additions & 14 deletions analysis/data_sets_I/run_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,19 +17,19 @@
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
# met:
#
# * Redistributions of source code must retain the above copyright
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
Expand All @@ -45,7 +45,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#

import gzip, cPickle, math, sys, os, os.path
import gzip, pickle, math, sys, os, os.path
import numpy as np
from scipy import special, stats
from collections import defaultdict
Expand Down Expand Up @@ -92,7 +92,7 @@

# loop over dataset sources
for dataset in conf.set_data.keys():
print dataset
print( dataset)
# output directories and input directory
outdir = outpath+'/'+dataset
if not os.path.exists(outdir): os.makedirs(outdir)
Expand All @@ -101,13 +101,13 @@
inpath = tmppath+'/'+dataset

# loop over targets
for target in conf.set_data:
print target
for target in conf.set_data[dataset]['ids']:
print( target)

# load results
validation = cPickle.load(gzip.open(inpath+'/validation_'+str(target)+'.pkl.gz', 'r'))
methodkeys = validation.keys()
fpkeys = validation[methodkeys[0]].keys()
validation = pickle.load(gzip.open(inpath+'/validation_'+str(target)+'.pkl.gz', 'rb'))
methodkeys = list(validation.keys())
fpkeys = list(validation[methodkeys[0]].keys())

# if ranks is not yet set: prepare it
if len(ranks) == 0:
Expand Down
22 changes: 11 additions & 11 deletions analysis/data_sets_I/run_fp_summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,19 +15,19 @@
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
# met:
#
# * Redistributions of source code must retain the above copyright
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
Expand All @@ -43,7 +43,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#

import gzip, cPickle, sys, os, os.path
import gzip, pickle, sys, os, os.path
from collections import defaultdict
from optparse import OptionParser

Expand Down Expand Up @@ -81,17 +81,17 @@

# loop over dataset sources
for dataset in conf.set_data.keys():
print dataset
print( dataset)
# input path
inpath = outpath+'/'+dataset

# loop over targets
for target in conf.set_data[dataset]['ids']:
print target
print( target)

# load results
results, fpkeys = ana_func.readFile(open(inpath+'/target_'+str(target)+'.txt', 'r'))
methodkeys = results.keys()
methodkeys = list(results.keys())

# if summary is not yet set: prepare it
if len(summary) == 0:
Expand Down
22 changes: 11 additions & 11 deletions analysis/data_sets_I/run_method_summary.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,19 +15,19 @@
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
# met:
#
# * Redistributions of source code must retain the above copyright
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
Expand All @@ -43,7 +43,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#

import gzip, cPickle, sys, os, os.path
import gzip, pickle, sys, os, os.path
from collections import defaultdict
from optparse import OptionParser

Expand Down Expand Up @@ -81,17 +81,17 @@

# loop over dataset sources
for dataset in conf.set_data.keys():
print dataset
print( dataset)
# input directory
inpath = outpath+'/'+dataset

# loop over targets
for target in conf.set_data[dataset]['ids']:
print target
print( target)

# load results
results, fpkeys = ana_func.readFile(open(inpath+'/target_'+str(target)+'.txt', 'r'))
methodkeys = results.keys()
methodkeys = list(results.keys())

# if summary is not yet set: prepare it
if len(summary) == 0:
Expand Down
22 changes: 11 additions & 11 deletions analysis/data_sets_II/run_analysis.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,19 +17,19 @@
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
# met:
#
# * Redistributions of source code must retain the above copyright
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
Expand All @@ -45,7 +45,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#

import gzip, cPickle, math, sys, os, os.path
import gzip, pickle, math, sys, os, os.path
import numpy as np
from scipy import special, stats
from collections import defaultdict
Expand Down Expand Up @@ -99,11 +99,11 @@

# loop over targets
for target in conf.set_data:
print target
print( target)

# load results
validation = cPickle.load(gzip.open(inpath+'/validation_'+str(target)+'.pkl.gz', 'r'))
methodkeys = validation.keys()
validation = pickle.load(gzip.open(inpath+'/validation_'+str(target)+'.pkl.gz', 'rb'))
methodkeys = list(validation.keys())
fpkeys = validation[methodkeys[0]].keys()

# if ranks is not yet set: prepare it
Expand Down
20 changes: 10 additions & 10 deletions analysis/data_sets_II/run_fp_summary.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,19 +15,19 @@
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
# met:
#
# * Redistributions of source code must retain the above copyright
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
Expand All @@ -43,7 +43,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#

import gzip, cPickle, sys, os, os.path
import gzip, pickle, sys, os, os.path
from collections import defaultdict
from optparse import OptionParser

Expand Down Expand Up @@ -84,11 +84,11 @@

# loop over targets
for target in conf.set_data:
print target
print( target)

# load results
results, fpkeys = ana_func.readFile(open(inpath+'/target_'+str(target)+'.txt', 'r'))
methodkeys = results.keys()
methodkeys = list(results.keys())

# if summary is not yet set: prepare it
if len(summary) == 0:
Expand Down
18 changes: 9 additions & 9 deletions analysis/data_sets_II/run_method_summary.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,19 +15,19 @@
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
# met:
#
# * Redistributions of source code must retain the above copyright
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
Expand All @@ -43,7 +43,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#

import gzip, cPickle, sys, os, os.path
import gzip, pickle, sys, os, os.path
from collections import defaultdict
from optparse import OptionParser

Expand Down Expand Up @@ -84,7 +84,7 @@

# loop over targets
for target in conf.set_data:
print target
print( target)

# load results
results, fpkeys = ana_func.readFile(open(inpath+'/target_'+str(target)+'.txt', 'r'))
Expand Down
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