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@sandipchatterjee
sandipchatterjee committed Aug 29, 2023
1 parent 39ab273 commit 929c135
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Showing 25 changed files with 11,747 additions and 8,847 deletions.
1,350 changes: 943 additions & 407 deletions examples/borzoi_helpers.py
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623 changes: 349 additions & 274 deletions src/scripts/borzoi_bench_crispr.py
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381 changes: 208 additions & 173 deletions src/scripts/borzoi_bench_crispr_folds.py
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476 changes: 265 additions & 211 deletions src/scripts/borzoi_bench_flowfish_folds.py
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619 changes: 337 additions & 282 deletions src/scripts/borzoi_bench_gasperini_folds.py
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891 changes: 496 additions & 395 deletions src/scripts/borzoi_bench_ipaqtl_folds.py
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891 changes: 496 additions & 395 deletions src/scripts/borzoi_bench_paqtl_folds.py
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969 changes: 534 additions & 435 deletions src/scripts/borzoi_bench_sqtl_folds.py
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365 changes: 219 additions & 146 deletions src/scripts/borzoi_bench_trip_folds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,163 +28,236 @@
# main
################################################################################
def main():
usage = 'usage: %prog [options] <params_file> <data_dir> <promoter_file> <insertions_file>'
parser = OptionParser(usage)

# trip
trip_options = OptionGroup(parser, 'borzoi_trip.py options')
trip_options.add_option('-f', dest='genome_fasta',
default='%s/assembly/ucsc/hg38.fa' % os.environ['HG38'],
help='Genome FASTA for sequences [Default: %default]')
trip_options.add_option('-o',dest='out_dir',
default='trip',
help='Output directory for tables and plots [Default: %default]')
trip_options.add_option('--site', dest='site',
default=False, action='store_true',
help='Return the insertion site without the promoter [Default: %default]')
trip_options.add_option('--reporter', dest='reporter',
default=False, action='store_true',
help='Insert the flanking piggyback reporter with the promoter [Default: %default]')
trip_options.add_option('--reporter_bare', dest='reporter_bare',
default=False, action='store_true',
help='Insert the flanking piggyback reporter with the promoter (no terminal repeats) [Default: %default]')
trip_options.add_option('--rc', dest='rc',
default=False, action='store_true',
help='Average forward and reverse complement predictions [Default: %default]')
trip_options.add_option('--shifts', dest='shifts',
default='0', type='str',
help='Ensemble prediction shifts [Default: %default]')
trip_options.add_option('-t', dest='targets_file',
default=None, type='str',
help='File specifying target indexes and labels in table format')
parser.add_option_group(trip_options)

# cross-fold
fold_options = OptionGroup(parser, 'cross-fold options')
fold_options.add_option('-c', dest='crosses',
default=1, type='int',
help='Number of cross-fold rounds [Default:%default]')
fold_options.add_option('-d', dest='data_head',
default=None, type='int',
help='Index for dataset/head [Default: %default]')
fold_options.add_option('-e', dest='conda_env',
default='tf210',
help='Anaconda environment [Default: %default]')
fold_options.add_option('--name', dest='name',
default='trip', help='SLURM name prefix [Default: %default]')
fold_options.add_option('--max_proc', dest='max_proc',
default=None, type='int',
help='Maximum concurrent processes [Default: %default]')
fold_options.add_option('-q', dest='queue',
default='geforce',
help='SLURM queue on which to run the jobs [Default: %default]')
fold_options.add_option('-r', dest='restart',
default=False, action='store_true',
help='Restart a partially completed job [Default: %default]')
parser.add_option_group(fold_options)

(options, args) = parser.parse_args()

if len(args) != 4:
print(len(args))
print(args)
parser.error('Must provide parameters file, cross-fold directory, TRIP promoter sequences, and TRIP insertion sites')
else:
params_file = args[0]
exp_dir = args[1]
promoters_file = args[2]
insertions_file = args[3]

#######################################################
# prep work

# count folds
num_folds = 0
fold0_dir = '%s/f%dc0' % (exp_dir, num_folds)
model_file = '%s/train/model_best.h5' % fold0_dir
if options.data_head is not None:
model_file = '%s/train/model%d_best.h5' % (fold0_dir, options.data_head)
while os.path.isfile(model_file):
num_folds += 1
fold0_dir = '%s/f%dc0' % (exp_dir, num_folds)
model_file = '%s/train/model_best.h5' % fold0_dir
usage = "usage: %prog [options] <params_file> <data_dir> <promoter_file> <insertions_file>"
parser = OptionParser(usage)

# trip
trip_options = OptionGroup(parser, "borzoi_trip.py options")
trip_options.add_option(
"-f",
dest="genome_fasta",
default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"],
help="Genome FASTA for sequences [Default: %default]",
)
trip_options.add_option(
"-o",
dest="out_dir",
default="trip",
help="Output directory for tables and plots [Default: %default]",
)
trip_options.add_option(
"--site",
dest="site",
default=False,
action="store_true",
help="Return the insertion site without the promoter [Default: %default]",
)
trip_options.add_option(
"--reporter",
dest="reporter",
default=False,
action="store_true",
help="Insert the flanking piggyback reporter with the promoter [Default: %default]",
)
trip_options.add_option(
"--reporter_bare",
dest="reporter_bare",
default=False,
action="store_true",
help="Insert the flanking piggyback reporter with the promoter (no terminal repeats) [Default: %default]",
)
trip_options.add_option(
"--rc",
dest="rc",
default=False,
action="store_true",
help="Average forward and reverse complement predictions [Default: %default]",
)
trip_options.add_option(
"--shifts",
dest="shifts",
default="0",
type="str",
help="Ensemble prediction shifts [Default: %default]",
)
trip_options.add_option(
"-t",
dest="targets_file",
default=None,
type="str",
help="File specifying target indexes and labels in table format",
)
parser.add_option_group(trip_options)

# cross-fold
fold_options = OptionGroup(parser, "cross-fold options")
fold_options.add_option(
"-c",
dest="crosses",
default=1,
type="int",
help="Number of cross-fold rounds [Default:%default]",
)
fold_options.add_option(
"-d",
dest="data_head",
default=None,
type="int",
help="Index for dataset/head [Default: %default]",
)
fold_options.add_option(
"-e",
dest="conda_env",
default="tf210",
help="Anaconda environment [Default: %default]",
)
fold_options.add_option(
"--name",
dest="name",
default="trip",
help="SLURM name prefix [Default: %default]",
)
fold_options.add_option(
"--max_proc",
dest="max_proc",
default=None,
type="int",
help="Maximum concurrent processes [Default: %default]",
)
fold_options.add_option(
"-q",
dest="queue",
default="geforce",
help="SLURM queue on which to run the jobs [Default: %default]",
)
fold_options.add_option(
"-r",
dest="restart",
default=False,
action="store_true",
help="Restart a partially completed job [Default: %default]",
)
parser.add_option_group(fold_options)

(options, args) = parser.parse_args()

if len(args) != 4:
print(len(args))
print(args)
parser.error(
"Must provide parameters file, cross-fold directory, TRIP promoter sequences, and TRIP insertion sites"
)
else:
params_file = args[0]
exp_dir = args[1]
promoters_file = args[2]
insertions_file = args[3]

#######################################################
# prep work

# count folds
num_folds = 0
fold0_dir = "%s/f%dc0" % (exp_dir, num_folds)
model_file = "%s/train/model_best.h5" % fold0_dir
if options.data_head is not None:
model_file = '%s/train/model%d_best.h5' % (fold0_dir, options.data_head)
print('Found %d folds' % num_folds)
if num_folds == 0:
exit(1)

################################################################
# TRIP prediction jobs

# command base
cmd_base = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd_base += ' conda activate %s;' % options.conda_env
cmd_base += ' echo $HOSTNAME;'

jobs = []

for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%dc%d' % (exp_dir, fi, ci)
name = '%s-f%dc%d' % (options.name, fi, ci)

# update output directory
it_out_dir = '%s/%s' % (it_dir, options.out_dir)
os.makedirs(it_out_dir, exist_ok=True)

model_file = '%s/train/model_best.h5' % it_dir
if options.data_head is not None:
model_file = '%s/train/model%d_best.h5' % (it_dir, options.data_head)

cmd_fold = '%s time borzoi_trip.py %s %s %s %s' % (cmd_base, params_file, model_file, promoters_file, insertions_file)

# TRIP job
job_out_dir = it_out_dir
if not options.restart or not os.path.isfile('%s/preds.h5'%job_out_dir):
cmd_job = cmd_fold
cmd_job += ' %s' % options_string(options, trip_options, job_out_dir)
j = slurm.Job(cmd_job, name,
'%s.out'%job_out_dir, '%s.err'%job_out_dir,
queue=options.queue, gpu=1,
mem=60000, time='7-0:0:0')
jobs.append(j)

slurm.multi_run(jobs, max_proc=options.max_proc, verbose=True,
launch_sleep=10, update_sleep=60)
model_file = "%s/train/model%d_best.h5" % (fold0_dir, options.data_head)
while os.path.isfile(model_file):
num_folds += 1
fold0_dir = "%s/f%dc0" % (exp_dir, num_folds)
model_file = "%s/train/model_best.h5" % fold0_dir
if options.data_head is not None:
model_file = "%s/train/model%d_best.h5" % (fold0_dir, options.data_head)
print("Found %d folds" % num_folds)
if num_folds == 0:
exit(1)

################################################################
# TRIP prediction jobs

# command base
cmd_base = ". /home/drk/anaconda3/etc/profile.d/conda.sh;"
cmd_base += " conda activate %s;" % options.conda_env
cmd_base += " echo $HOSTNAME;"

jobs = []

for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = "%s/f%dc%d" % (exp_dir, fi, ci)
name = "%s-f%dc%d" % (options.name, fi, ci)

# update output directory
it_out_dir = "%s/%s" % (it_dir, options.out_dir)
os.makedirs(it_out_dir, exist_ok=True)

model_file = "%s/train/model_best.h5" % it_dir
if options.data_head is not None:
model_file = "%s/train/model%d_best.h5" % (it_dir, options.data_head)

cmd_fold = "%s time borzoi_trip.py %s %s %s %s" % (
cmd_base,
params_file,
model_file,
promoters_file,
insertions_file,
)

# TRIP job
job_out_dir = it_out_dir
if not options.restart or not os.path.isfile("%s/preds.h5" % job_out_dir):
cmd_job = cmd_fold
cmd_job += " %s" % options_string(options, trip_options, job_out_dir)
j = slurm.Job(
cmd_job,
name,
"%s.out" % job_out_dir,
"%s.err" % job_out_dir,
queue=options.queue,
gpu=1,
mem=60000,
time="7-0:0:0",
)
jobs.append(j)

slurm.multi_run(
jobs, max_proc=options.max_proc, verbose=True, launch_sleep=10, update_sleep=60
)


def options_string(options, group_options, rep_dir):
options_str = ''
options_str = ""

for opt in group_options.option_list:
opt_str = opt.get_opt_string()
opt_value = options.__dict__[opt.dest]

for opt in group_options.option_list:
opt_str = opt.get_opt_string()
opt_value = options.__dict__[opt.dest]
# wrap askeriks in ""
if type(opt_value) == str and opt_value.find("*") != -1:
opt_value = '"%s"' % opt_value

# wrap askeriks in ""
if type(opt_value) == str and opt_value.find('*') != -1:
opt_value = '"%s"' % opt_value
# no value for bools
elif type(opt_value) == bool:
if not opt_value:
opt_str = ""
opt_value = ""

# no value for bools
elif type(opt_value) == bool:
if not opt_value:
opt_str = ''
opt_value = ''
# skip Nones
elif opt_value is None:
opt_str = ""
opt_value = ""

# skip Nones
elif opt_value is None:
opt_str = ''
opt_value = ''
# modify
elif opt.dest == "out_dir":
opt_value = rep_dir

# modify
elif opt.dest == 'out_dir':
opt_value = rep_dir
options_str += " %s %s" % (opt_str, opt_value)

options_str += ' %s %s' % (opt_str, opt_value)
return options_str

return options_str

################################################################################
# __main__
################################################################################
if __name__ == '__main__':
main()
if __name__ == "__main__":
main()
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