def from_mdir(cls, model_dir):
from basepair.seqmodel import SeqModel
# TODO - figure out also the fasta_file if present (from dataspec)
from basepair.cli.schemas import DataSpec
ds_path = os.path.join(model_dir, "dataspec.yaml")
if os.path.exists(ds_path):
ds = DataSpec.load(ds_path)
fasta_file = ds.fasta_file
else:
fasta_file = None
return cls(SeqModel.from_mdir(model_dir), fasta_file=fasta_file)
def load_data(model_dir, cache_data=False,
dataspec=None, hparams=None, data=None, preprocessor=None):
if dataspec is not None:
ds = DataSpec.load(dataspec)
else:
ds = DataSpec.load(os.path.join(model_dir, "dataspec.yaml"))
if hparams is not None:
hp = HParams.load(hparams)
else:
hp = HParams.load(os.path.join(model_dir, "hparams.yaml"))
if data is not None:
data_path = data
else:
data_path = os.path.join(model_dir, 'data.pkl')
if os.path.exists(data_path):
train, valid, test = read_pkl(data_path)
else:
train, valid, test = chip_exo_nexus(ds,
peak_width=hp.data.peak_width,
shuffle=hp.data.shuffle,
valid_chr=hp.data.valid_chr,
test_chr=hp.data.test_chr)
# Pre-process the data
logger.info("Pre-processing the data")
if preprocessor is not None:
preproc_path = os.path.join(model_dir, "preprocessor.pkl")
else:
preproc_path = preprocessor
preproc = read_pkl(preproc_path)
train[1] = preproc.transform(train[1])
valid[1] = preproc.transform(valid[1])
try:
test[1] = preproc.transform(test[1])
except Exception:
logger.warn("Test set couldn't be processed")
test = None
return train, valid, test
def get_StrandedProfile_datasets(dataspec,
peak_width=200,
seq_width=None,
shuffle=True,
target_transformer=AppendCounts(),
valid_chr=['chr2', 'chr3', 'chr4'],
test_chr=['chr1', 'chr8', 'chr9'],
all_chr=all_chr,
exclude_chr=[],
vmtouch=True):
# test and valid shouldn't be in the valid or test sets
for vc in valid_chr:
assert vc not in exclude_chr
for vc in test_chr:
assert vc not in exclude_chr
if isinstance(dataspec, str):
dataspec = DataSpec.load(dataspec)
if vmtouch:
# use vmtouch to load all file to memory
dataspec.touch_all_files()
return (
StrandedProfile(
dataspec,
peak_width,
seq_width=seq_width,
# Only include chromosomes from `all_chr`
incl_chromosomes=[
c for c in all_chr
if c not in valid_chr + test_chr + exclude_chr
],
excl_chromosomes=valid_chr + test_chr + exclude_chr,
shuffle=shuffle,
target_transformer=target_transformer),
StrandedProfile(dataspec,
peak_width,
seq_width=seq_width,
incl_chromosomes=valid_chr,
shuffle=shuffle,
target_transformer=target_transformer),
StrandedProfile(dataspec,
peak_width,
seq_width=seq_width,
incl_chromosomes=test_chr,
shuffle=shuffle,
target_transformer=target_transformer))
def dataspec():
return DataSpec(bigwigs={
"task1":
TaskSpec(
task='task1',
pos_counts=f"{ddir}/pos.bw",
neg_counts=f"{ddir}/neg.bw",
),
"task2":
TaskSpec(
task='task2',
pos_counts=f"{ddir}/pos.bw",
neg_counts=f"{ddir}/neg.bw",
)
},
fasta_file=f"{ddir}/ref.fa",
peaks=f"{ddir}/peaks.bed")
def from_mdir(cls, model_dir):
"""
Args:
model_dir (str): Path to the model directory
"""
import os
from basepair.cli.schemas import DataSpec
from keras.models import load_model
from basepair.utils import read_pkl
ds = DataSpec.load(os.path.join(model_dir, "dataspec.yaml"))
model = load_model(os.path.join(model_dir, "model.h5"))
preproc_file = os.path.join(model_dir, "preprocessor.pkl")
if os.path.exists(preproc_file):
preproc = read_pkl(preproc_file)
else:
preproc = None
return cls(model=model, fasta_file=ds.fasta_file, tasks=list(ds.task_specs), preproc=preproc)
def __init__(self,
ds,
peak_width=200,
seq_width=None,
incl_chromosomes=None,
excl_chromosomes=None,
intervals_file=None,
bcolz=False,
in_memory=False,
include_metadata=True,
taskname_first=False,
tasks=None,
include_classes=False,
only_classes=False,
shuffle=True,
interval_transformer=None,
target_transformer=None,
profile_bias_pool_size=None):
"""Dataset for loading the bigwigs and fastas
Args:
ds (basepair.src.schemas.DataSpec): data specification containing the
fasta file, bed files and bigWig file paths
chromosomes (list of str): a list of chor
peak_width: resize the bed file to a certain width
intervals_file: if specified, use these regions to train the model.
If not specified, the regions are inferred from the dataspec.
only_classes: if True, load only classes
bcolz: If True, the bigwig/fasta files are in the genomelake bcolz format
in_memory: If True, load the whole bcolz into memory. Only applicable when bcolz=True
shuffle: True
preprocessor: trained preprocessor object containing the .transform methods
"""
if isinstance(ds, str):
self.ds = DataSpec.load(ds)
else:
self.ds = ds
self.peak_width = peak_width
if seq_width is None:
self.seq_width = peak_width
else:
self.seq_width = seq_width
self.shuffle = shuffle
self.intervals_file = intervals_file
self.incl_chromosomes = incl_chromosomes
self.excl_chromosomes = excl_chromosomes
self.target_transformer = target_transformer
self.include_classes = include_classes
self.only_classes = only_classes
self.taskname_first = taskname_first
if self.only_classes:
assert self.include_classes
self.profile_bias_pool_size = profile_bias_pool_size
# not specified yet
self.fasta_extractor = None
self.bw_extractors = None
self.bias_bw_extractors = None
self.include_metadata = include_metadata
self.interval_transformer = interval_transformer
self.bcolz = bcolz
self.in_memory = in_memory
if not self.bcolz and self.in_memory:
raise ValueError(
"in_memory option only applicable when bcolz=True")
# Load chromosome lengths
if self.bcolz:
p = json.loads(
(Path(self.ds.fasta_file) / "metadata.json").read_text())
self.chrom_lens = {c: v[0] for c, v in p['file_shapes'].items()}
else:
fa = FastaFile(self.ds.fasta_file)
self.chrom_lens = {
name: l
for name, l in zip(fa.references, fa.lengths)
}
if len(self.chrom_lens) == 0:
raise ValueError(
f"no chromosomes found in fasta file: {self.ds.fasta_file}. "
"Make sure the file path is correct and that the fasta index file {self.ds.fasta_file}.fai is up to date"
)
del fa
if self.intervals_file is None:
self.dfm = load_beds(bed_files={
task: task_spec.peaks
for task, task_spec in self.ds.task_specs.items()
if task_spec.peaks is not None
},
chromosome_lens=self.chrom_lens,
excl_chromosomes=self.excl_chromosomes,
incl_chromosomes=self.incl_chromosomes,
resize_width=max(self.peak_width,
self.seq_width))
assert list(
self.dfm.columns)[:4] == ["chrom", "start", "end", "task"]
if self.shuffle:
self.dfm = self.dfm.sample(frac=1)
self.tsv = None
self.dfm_tasks = None
else:
self.tsv = TsvReader(self.intervals_file,
num_chr=False,
label_dtype=int,
mask_ambigous=-1,
incl_chromosomes=incl_chromosomes,
excl_chromosomes=excl_chromosomes,
chromosome_lens=self.chrom_lens,
resize_width=max(self.peak_width,
self.seq_width))
if self.shuffle:
self.tsv.shuffle_inplace()
self.dfm = self.tsv.df # use the data-frame from tsv
self.dfm_tasks = self.tsv.get_target_names()
# remember the tasks
if tasks is None:
self.tasks = list(self.ds.task_specs)
else:
self.tasks = tasks
if self.bcolz and self.in_memory:
self.fasta_extractor = ArrayExtractor(self.ds.fasta_file,
in_memory=True)
self.bw_extractors = {
task: [
ArrayExtractor(task_spec.pos_counts, in_memory=True),
ArrayExtractor(task_spec.neg_counts, in_memory=True)
]
for task, task_spec in self.ds.task_specs.items()
if task in self.tasks
}
self.bias_bw_extractors = {
task: [
ArrayExtractor(task_spec.pos_counts, in_memory=True),
ArrayExtractor(task_spec.neg_counts, in_memory=True)
]
for task, task_spec in self.ds.bias_specs.items()
if task in self.tasks
}
if self.include_classes:
assert self.dfm_tasks is not None
if self.dfm_tasks is not None:
assert set(self.tasks).issubset(self.dfm_tasks)
# setup bias maps per task
self.task_bias_tracks = {
task: [
bias for bias, spec in self.ds.bias_specs.items()
if task in spec.tasks
]
for task in self.tasks
}
def get_gw_StrandedProfile_datasets(dataspec,
intervals_file=None,
peak_width=200,
seq_width=None,
shuffle=True,
target_transformer=AppendCounts(),
include_metadata=False,
taskname_first=False,
include_classes=False,
only_classes=False,
tasks=None,
valid_chr=['chr2', 'chr3', 'chr4'],
test_chr=['chr1', 'chr8', 'chr9'],
exclude_chr=[],
vmtouch=True,
profile_bias_pool_size=None):
# NOTE = only chromosomes from chr1-22 and chrX and chrY are considered here
# (e.g. all other chromosomes like ChrUn... are omitted)
from basepair.metrics import BPNetMetric, PeakPredictionProfileMetric, pearson_spearman
# test and valid shouldn't be in the valid or test sets
for vc in valid_chr:
assert vc not in exclude_chr
for vc in test_chr:
assert vc not in exclude_chr
dataspec = DataSpec.load(dataspec)
if vmtouch:
# use vmtouch to load all file to memory
dataspec.touch_all_files()
if tasks is None:
tasks = list(dataspec.task_specs)
train = StrandedProfile(
dataspec,
peak_width,
seq_width=seq_width,
intervals_file=intervals_file,
include_metadata=include_metadata,
taskname_first=taskname_first,
include_classes=include_classes,
only_classes=only_classes,
tasks=tasks,
incl_chromosomes=[
c for c in all_chr if c not in valid_chr + test_chr + exclude_chr
],
excl_chromosomes=valid_chr + test_chr + exclude_chr,
shuffle=shuffle,
target_transformer=target_transformer,
profile_bias_pool_size=profile_bias_pool_size)
valid = [('train-valid-genome-wide',
StrandedProfile(dataspec,
peak_width,
seq_width=seq_width,
intervals_file=intervals_file,
include_metadata=include_metadata,
include_classes=include_classes,
only_classes=only_classes,
taskname_first=taskname_first,
tasks=tasks,
incl_chromosomes=valid_chr,
shuffle=shuffle,
target_transformer=target_transformer,
profile_bias_pool_size=profile_bias_pool_size))]
if include_classes:
# Only use binary classification for genome-wide evaluation
valid = valid + [('valid-genome-wide',
StrandedProfile(
dataspec,
peak_width,
seq_width=seq_width,
intervals_file=intervals_file,
include_metadata=include_metadata,
include_classes=True,
only_classes=True,
taskname_first=taskname_first,
tasks=tasks,
incl_chromosomes=valid_chr,
shuffle=shuffle,
target_transformer=target_transformer,
profile_bias_pool_size=profile_bias_pool_size))]
if not only_classes:
# Add also the peak regions
valid = valid + [
(
'valid-peaks',
StrandedProfile(
dataspec,
peak_width,
seq_width=seq_width,
intervals_file=None,
include_metadata=include_metadata,
taskname_first=taskname_first,
tasks=tasks,
include_classes=False, # dataspec doesn't contain labels
only_classes=only_classes,
incl_chromosomes=valid_chr,
shuffle=shuffle,
target_transformer=target_transformer,
profile_bias_pool_size=profile_bias_pool_size)),
(
'train-peaks',
StrandedProfile(
dataspec,
peak_width,
seq_width=seq_width,
intervals_file=None,
include_metadata=include_metadata,
taskname_first=taskname_first,
tasks=tasks,
include_classes=False, # dataspec doesn't contain labels
only_classes=only_classes,
incl_chromosomes=[
c for c in all_chr
if c not in valid_chr + test_chr + exclude_chr
],
excl_chromosomes=valid_chr + test_chr + exclude_chr,
shuffle=shuffle,
target_transformer=target_transformer,
profile_bias_pool_size=profile_bias_pool_size)),
# use the default metric for the peak sets
]
return train, valid
def get_StrandedProfile_datasets2(dataspec,
peak_width=200,
intervals_file=None,
seq_width=None,
shuffle=True,
target_transformer=AppendCounts(),
include_metadata=False,
valid_chr=['chr2', 'chr3', 'chr4'],
test_chr=['chr1', 'chr8', 'chr9'],
tasks=None,
taskname_first=False,
exclude_chr=[],
augment_interval=False,
interval_augmentation_shift=200,
vmtouch=True,
profile_bias_pool_size=None):
from basepair.metrics import BPNetMetric, PeakPredictionProfileMetric, pearson_spearman
# test and valid shouldn't be in the valid or test sets
for vc in valid_chr:
assert vc not in exclude_chr
for vc in test_chr:
assert vc not in exclude_chr
dataspec = DataSpec.load(dataspec)
if vmtouch:
# use vmtouch to load all file to memory
dataspec.touch_all_files()
if tasks is None:
tasks = list(dataspec.task_specs)
if augment_interval:
interval_transformer = IntervalAugmentor(
max_shift=interval_augmentation_shift, flip_strand=True)
else:
interval_transformer = None
return (StrandedProfile(
dataspec,
peak_width,
intervals_file=intervals_file,
seq_width=seq_width,
include_metadata=include_metadata,
incl_chromosomes=[
c for c in all_chr if c not in valid_chr + test_chr + exclude_chr
],
excl_chromosomes=valid_chr + test_chr + exclude_chr,
tasks=tasks,
taskname_first=taskname_first,
shuffle=shuffle,
target_transformer=target_transformer,
interval_transformer=interval_transformer,
profile_bias_pool_size=profile_bias_pool_size), [
('valid-peaks',
StrandedProfile(dataspec,
peak_width,
intervals_file=intervals_file,
seq_width=seq_width,
include_metadata=include_metadata,
incl_chromosomes=valid_chr,
tasks=tasks,
taskname_first=taskname_first,
interval_transformer=interval_transformer,
shuffle=shuffle,
target_transformer=target_transformer,
profile_bias_pool_size=profile_bias_pool_size)),
('train-peaks',
StrandedProfile(dataspec,
peak_width,
intervals_file=intervals_file,
seq_width=seq_width,
include_metadata=include_metadata,
incl_chromosomes=[
c for c in all_chr
if c not in valid_chr + test_chr + exclude_chr
],
excl_chromosomes=valid_chr + test_chr +
exclude_chr,
tasks=tasks,
taskname_first=taskname_first,
interval_transformer=interval_transformer,
shuffle=shuffle,
target_transformer=target_transformer,
profile_bias_pool_size=profile_bias_pool_size)),
])
def evaluate(model_dir,
output_dir=None,
gpu=0,
exclude_metrics=False,
splits=['train', 'valid'],
model_path=None,
data=None,
hparams=None,
dataspec=None,
preprocessor=None):
"""
Args:
model_dir: path to the model directory
splits: For which data splits to compute the evaluation metrics
model_metrics: if True, metrics computed using mode.evaluate(..)
"""
if gpu is not None:
create_tf_session(gpu)
if dataspec is not None:
ds = DataSpec.load(dataspec)
else:
ds = DataSpec.load(os.path.join(model_dir, "dataspec.yaml"))
if hparams is not None:
hp = HParams.load(hparams)
else:
hp = HParams.load(os.path.join(model_dir, "hparams.yaml"))
if model_path is not None:
model = load_model(model_path)
else:
model = load_model(os.path.join(model_dir, "model.h5"))
if output_dir is None:
output_dir = os.path.join(model_dir, "eval")
train, valid, test = load_data(model_dir,
dataspec=dataspec,
hparams=hparams,
data=data,
preprocessor=preprocessor)
data = dict(train=train, valid=valid, test=test)
metrics = {}
profile_metrics = []
os.makedirs(os.path.join(output_dir, "plots"),
exist_ok=True)
for split in tqdm(splits):
y_pred = model.predict(data[split][0])
y_true = data[split][1]
if not exclude_metrics:
eval_metrics_values = model.evaluate(data[split][0],
data[split][1])
eval_metrics = dict(zip(_listify(model.metrics_names),
_listify(eval_metrics_values)))
eval_metrics = {split + "/" + k.replace("_", "/"): v
for k, v in eval_metrics.items()}
metrics = {**eval_metrics, **metrics}
for task in ds.task_specs:
# Counts
yp = y_pred[ds.task2idx(task, "counts")].sum(axis=-1)
yt = y_true["counts/" + task].sum(axis=-1)
# compute the correlation
rp = pearsonr(yt, yp)[0]
rs = spearmanr(yt, yp)[0]
metrics = {**metrics,
split + f"/counts/{task}/pearsonr": rp,
split + f"/counts/{task}/spearmanr": rs,
}
fig = plt.figure(figsize=(5, 5))
plt.scatter(yp, yt, alpha=0.5)
plt.xlabel("Predicted")
plt.ylabel("Observed")
plt.title(f"R_pearson={rp:.2f}, R_spearman={rs:.2f}")
plt.savefig(os.path.join(output_dir, f"plots/counts.{split}.{task}.png"))
# Profile
yp = softmax(y_pred[ds.task2idx(task, "profile")])
yt = y_true["profile/" + task]
df = eval_profile(yt, yp,
pos_min_threshold=hp.evaluate.pos_min_threshold,
neg_max_threshold=hp.evaluate.neg_max_threshold,
required_min_pos_counts=hp.evaluate.required_min_pos_counts,
binsizes=hp.evaluate.binsizes)
df['task'] = task
df['split'] = split
# Evaluate for the smallest binsize
auprc_min = df[df.binsize == min(hp.evaluate.binsizes)].iloc[0].auprc
metrics[split + f'/profile/{task}/auprc'] = auprc_min
profile_metrics.append(df)
# Write the count metrics
write_json(metrics, os.path.join(output_dir, "metrics.json"))
# write the profile metrics
dfm = pd.concat(profile_metrics)
dfm.to_csv(os.path.join(output_dir, "profile_metrics.tsv"),
sep='\t', index=False)
return dfm, metrics
def imp_score(model_dir,
output_file,
method="grad",
split='all',
batch_size=512,
num_workers=10,
h5_chunk_size=512,
max_batches=-1,
shuffle_seq=False,
memfrac=0.45,
exclude_chr='',
overwrite=False,
gpu=None):
"""Run importance scores for a BPNet model
Args:
model_dir: path to the model directory
output_file: output file path (HDF5 format)
method: which importance scoring method to use ('grad', 'deeplift' or 'ism')
split: for which dataset split to compute the importance scores
h5_chunk_size: hdf5 chunk size.
exclude_chr: comma-separated list of chromosomes to exclude
overwrite: if True, overwrite the output directory
gpu (int): which GPU to use locally. If None, GPU is not used
"""
add_file_logging(os.path.dirname(output_file), logger, 'modisco-score')
if gpu is not None:
create_tf_session(gpu, per_process_gpu_memory_fraction=memfrac)
else:
# Don't use any GPU's
os.environ['CUDA_VISIBLE_DEVICES'] = ''
if os.path.exists(output_file):
if overwrite:
os.remove(output_file)
else:
raise ValueError(f"File exists {output_file}. Use overwrite=True to overwrite it")
if exclude_chr:
exclude_chr = exclude_chr.split(",")
else:
exclude_chr = []
# load the config files
logger.info("Loading the config files")
model_dir = Path(model_dir)
hp = HParams.load(model_dir / "hparams.yaml")
ds = DataSpec.load(model_dir / "dataspec.yaml")
tasks = list(ds.task_specs)
# validate that the correct dataset was used
if hp.data.name != 'get_StrandedProfile_datasets':
logger.warn("hp.data.name != 'get_StrandedProfile_datasets'")
if split == 'valid':
assert len(exclude_chr) == 0
incl_chromosomes = hp.data.kwargs['valid_chr']
excl_chromosomes = None
elif split == 'test':
assert len(exclude_chr) == 0
incl_chromosomes = hp.data.kwargs['test_chr']
excl_chromosomes = None
elif split == 'train':
assert len(exclude_chr) == 0
incl_chromosomes = None
excl_chromosomes = hp.data.kwargs['valid_chr'] + hp.data.kwargs['test_chr'] + hp.data.kwargs.get('exclude_chr', [])
elif split == 'all':
incl_chromosomes = None
excl_chromosomes = hp.data.kwargs.get('exclude_chr', []) + exclude_chr
logger.info("Excluding chromosomes: {excl_chromosomes}")
else:
raise ValueError("split needs to be from {train,valid,test,all}")
logger.info("Creating the dataset")
from basepair.datasets import StrandedProfile
seq_len = hp.data.kwargs['peak_width']
dl_valid = StrandedProfile(ds,
incl_chromosomes=incl_chromosomes,
excl_chromosomes=excl_chromosomes,
peak_width=seq_len,
shuffle=False,
target_transformer=None)
bpnet = BPNet.from_mdir(model_dir)
writer = HDF5BatchWriter(output_file, chunk_size=h5_chunk_size)
for i, batch in enumerate(tqdm(dl_valid.batch_iter(batch_size=batch_size, num_workers=num_workers))):
if max_batches > 0:
logging.info(f"max_batches: {max_batches} exceeded. Stopping the computation")
if i > max_batches:
break
# append the bias model predictions
# (batch['inputs'], batch['targets']) = bm((batch['inputs'], batch['targets']))
# store the original batch containing 'inputs' and 'targets'
wdict = batch
if shuffle_seq:
# Di-nucleotide shuffle the sequences
if 'seq' in batch['inputs']:
batch['inputs']['seq'] = onehot_dinucl_shuffle(batch['inputs']['seq'])
else:
batch['inputs'] = onehot_dinucl_shuffle(batch['inputs'])
# loop through all tasks, pred_summary and strands
for task_i, task in enumerate(tasks):
for pred_summary in ['count', 'weighted']:
# figure out the number of channels
nstrands = batch['targets'][f'profile/{task}'].shape[-1]
strand_hash = ["pos", "neg"]
for strand_i in range(nstrands):
hyp_imp = bpnet.imp_score(batch['inputs'],
task=task,
strand=strand_hash[strand_i],
method=method,
pred_summary=pred_summary,
batch_size=None) # don't second-batch
# put importance scores to the dictionary
wdict[f"/hyp_imp/{task}/{pred_summary}/{strand_i}"] = hyp_imp
writer.batch_write(wdict)
writer.close()
def imp_score_seqmodel(model_dir,
output_file,
dataspec=None,
peak_width=1000,
seq_width=None,
intp_pattern='*', # specifies which imp. scores to compute
# skip_trim=False, # skip trimming the output
method="deeplift",
batch_size=512,
max_batches=-1,
shuffle_seq=False,
memfrac=0.45,
num_workers=10,
h5_chunk_size=512,
exclude_chr='',
include_chr='',
overwrite=False,
skip_bias=False,
gpu=None):
"""Run importance scores for a BPNet model
Args:
model_dir: path to the model directory
output_file: output file path (HDF5 format)
method: which importance scoring method to use ('grad', 'deeplift' or 'ism')
split: for which dataset split to compute the importance scores
h5_chunk_size: hdf5 chunk size.
exclude_chr: comma-separated list of chromosomes to exclude
overwrite: if True, overwrite the output directory
skip_bias: if True, don't store the bias tracks in teh output
gpu (int): which GPU to use locally. If None, GPU is not used
"""
add_file_logging(os.path.dirname(output_file), logger, 'modisco-score-seqmodel')
if gpu is not None:
create_tf_session(gpu, per_process_gpu_memory_fraction=memfrac)
else:
# Don't use any GPU's
os.environ['CUDA_VISIBLE_DEVICES'] = ''
if os.path.exists(output_file):
if overwrite:
os.remove(output_file)
else:
raise ValueError(f"File exists {output_file}. Use overwrite=True to overwrite it")
if seq_width is None:
logger.info("Using seq_width = peak_width")
seq_width = peak_width
# make sure these are int's
seq_width = int(seq_width)
peak_width = int(peak_width)
# Split
intp_patterns = intp_pattern.split(",")
# Allow chr inclusion / exclusion
if exclude_chr:
exclude_chr = exclude_chr.split(",")
else:
exclude_chr = None
if include_chr:
include_chr = include_chr.split(",")
else:
include_chr = None
logger.info("Loading the config files")
model_dir = Path(model_dir)
if dataspec is None:
# Specify dataspec
dataspec = model_dir / "dataspec.yaml"
ds = DataSpec.load(dataspec)
logger.info("Creating the dataset")
from basepair.datasets import StrandedProfile
dl_valid = StrandedProfile(ds,
incl_chromosomes=include_chr,
excl_chromosomes=exclude_chr,
peak_width=peak_width,
seq_width=seq_width,
shuffle=False,
taskname_first=True, # Required to work nicely with imp-score
target_transformer=None)
# Setup importance score trimming
if seq_width > peak_width:
# Trim
# make sure we can nicely trim the peak
logger.info("Trimming the output")
assert (seq_width - peak_width) % 2 == 0
trim_start = (seq_width - peak_width) // 2
trim_end = seq_width - trim_start
assert trim_end - trim_start == peak_width
elif seq_width == peak_width:
trim_start = 0
trim_end = peak_width
else:
raise ValueError("seq_width < peak_width")
seqmodel = SeqModel.from_mdir(model_dir)
# get all possible interpretation names
# make sure they match the specified glob
intp_names = [name for name, _ in seqmodel.get_intp_tensors(preact_only=False)
if fnmatch_any(name, intp_patterns)]
logger.info(f"Using the following interpretation targets:")
for n in intp_names:
print(n)
writer = HDF5BatchWriter(output_file, chunk_size=h5_chunk_size)
for i, batch in enumerate(tqdm(dl_valid.batch_iter(batch_size=batch_size, num_workers=num_workers))):
# store the original batch containing 'inputs' and 'targets'
wdict = batch
if skip_bias:
wdict['inputs'] = {'seq': wdict['inputs']['seq']} # ignore all other inputs
if max_batches > 0:
logging.info(f"max_batches: {max_batches} exceeded. Stopping the computation")
if i > max_batches:
break
if shuffle_seq:
# Di-nucleotide shuffle the sequences
batch['inputs']['seq'] = onehot_dinucl_shuffle(batch['inputs']['seq'])
for name in intp_names:
hyp_imp = seqmodel.imp_score(batch['inputs']['seq'],
name=name,
method=method,
batch_size=None) # don't second-batch
# put importance scores to the dictionary
# also trim the importance scores appropriately so that
# the output will always be w.r.t. the peak center
wdict[f"/hyp_imp/{name}"] = hyp_imp[:, trim_start:trim_end]
# trim the sequence as well
if isinstance(wdict['inputs'], dict):
# Trim the sequence
wdict['inputs']['seq'] = wdict['inputs']['seq'][:, trim_start:trim_end]
else:
wdict['inputs'] = wdict['inputs'][:, trim_start:trim_end]
writer.batch_write(wdict)
writer.close()
isf = ImpScoreFile(models_dir / exp / 'deeplift.imp_score.h5',
default_imp_score=imp_score)
dfi_subset = pd.read_parquet(
models_dir / exp / "deeplift/dfi_subset.parq",
engine='fastparquet').assign(model=model_name).assign(exp=exp)
mr = MultipleModiscoResult({
t: models_dir / exp / f'deeplift/{t}/out/{imp_score}/modisco.h5'
for t in get_tasks(exp)
})
return isf, dfi_subset, mr
# load DataSpec
# old config
rdir = get_repo_root()
dataspec_file = rdir / "src/chipnexus/train/seqmodel/ChIP-nexus.dataspec.yml"
ds = DataSpec.load(dataspec_file)
# Load all files into the page cache
logger.info("Touch all files")
ds.touch_all_files()
# --------------------------------------------
# ### nexus/profile
model_name = 'nexus/profile'
imp_score = 'profile/wn'
exp = models[model_name]
isf, dfi_subset, mr = load_data(model_name, imp_score, exp)
ranges_profile = isf.get_ranges()
profiles = isf.get_profiles()
# TODO - fix seqlets
dfi_list.append(
