def dataspec_stats(dataspec, regions=None, sample=None, peak_width=1000):
"""Compute the stats about the tracks
"""
import random
from pybedtools import BedTool
from bpnet.preproc import resize_interval
from genomelake.extractors import FastaExtractor
ds = DataSpec.load(dataspec)
if regions is not None:
regions = list(BedTool(regions))
else:
regions = ds.get_all_regions()
if sample is not None and sample < len(regions):
logger.info(
f"Using {sample} randomly sampled regions instead of {len(regions)}"
)
regions = random.sample(regions, k=sample)
# resize the regions
regions = [
resize_interval(interval, peak_width, ignore_strand=True)
for interval in regions
]
base_freq = FastaExtractor(ds.fasta_file)(regions).mean(axis=(0, 1))
count_stats = _track_stats(ds.load_counts(regions, progbar=True))
bias_count_stats = _track_stats(ds.load_bias_counts(regions, progbar=True))
print("")
print("Base frequency")
for i, base in enumerate(['A', 'C', 'G', 'T']):
print(f"- {base}: {base_freq[i]}")
print("")
print("Count stats")
for task, stats in count_stats.items():
print(f"- {task}")
for stat_key, stat_value in stats.items():
print(f" {stat_key}: {stat_value}")
print("")
print("Bias stats")
for task, stats in bias_count_stats.items():
print(f"- {task}")
for stat_key, stat_value in stats.items():
print(f" {stat_key}: {stat_value}")
lamb = np.mean([v["total median"] for v in count_stats.values()]) / 10
print("")
print(
f"We recommend to set lambda=total_count_median / 10 = {lamb:.2f} (default=10) in `bpnet train --override=` "
"to put 5x more weight on profile prediction than on total count prediction."
)
def from_mdir(cls, model_dir):
from bpnet.seqmodel import SeqModel
# figure out also the fasta_file if present (from dataspec)
from bpnet.dataspecs import DataSpec
ds_path = os.path.join(model_dir, "dataspec.yml")
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 bpnet_export_bw(
model_dir,
output_prefix,
fasta_file=None,
regions=None,
contrib_method='grad',
contrib_wildcard='*/profile/wn,*/counts/pre-act', # specifies which contrib. scores to compute
batch_size=256,
scale_contribution=False,
flip_negative_strand=False,
gpu=0,
memfrac_gpu=0.45):
"""Export model predictions and contribution scores to big-wig files
"""
from pybedtools import BedTool
from bpnet.modisco.core import Seqlet
output_dir = os.path.dirname(output_prefix)
add_file_logging(output_dir, logger, 'bpnet-export-bw')
os.makedirs(output_dir, exist_ok=True)
if gpu is not None:
create_tf_session(gpu, per_process_gpu_memory_fraction=memfrac_gpu)
logger.info("Load model")
bp = BPNetSeqModel.from_mdir(model_dir)
if regions is not None:
logger.info(
f"Computing predictions and contribution scores for provided regions: {regions}"
)
regions = list(BedTool(regions))
else:
logger.info("--regions not provided. Using regions from dataspec.yml")
ds = DataSpec.load(os.path.join(model_dir, 'dataspec.yml'))
regions = ds.get_all_regions()
seqlen = bp.input_seqlen()
logger.info(
f"Resizing regions (fix=center) to model's input width of: {seqlen}")
regions = [resize_interval(interval, seqlen) for interval in regions]
logger.info("Sort the bed file")
regions = list(BedTool(regions).sort())
bp.export_bw(regions=regions,
output_prefix=output_prefix,
contrib_method=contrib_method,
fasta_file=fasta_file,
pred_summaries=contrib_wildcard.replace("*/", "").split(","),
batch_size=batch_size,
scale_contribution=scale_contribution,
flip_negative_strand=flip_negative_strand,
chromosomes=None) # infer chromosomes from the fasta file
def bpnet_contrib(
model_dir,
output_file,
method="grad",
dataspec=None,
regions=None,
fasta_file=None, # alternative to dataspec
shuffle_seq=False,
shuffle_regions=False,
max_regions=None,
# reference='zeroes', # Currently the only option
# peak_width=1000, # automatically inferred from 'config.gin.json'
# seq_width=None,
contrib_wildcard='*/profile/wn,*/counts/pre-act', # specifies which contrib. scores to compute
batch_size=512,
gpu=0,
memfrac_gpu=0.45,
num_workers=10,
storage_chunk_size=512,
exclude_chr='',
include_chr='',
overwrite=False,
skip_bias=False):
"""Run contribution scores for a BPNet model
"""
from bpnet.extractors import _chrom_sizes
add_file_logging(os.path.dirname(output_file), logger, 'bpnet-contrib')
if gpu is not None:
create_tf_session(gpu, per_process_gpu_memory_fraction=memfrac_gpu)
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"
)
config = read_json(os.path.join(model_dir, 'config.gin.json'))
seq_width = config['seq_width']
peak_width = config['seq_width']
# NOTE - seq_width has to be the same for the input and the target
#
# infer from the command line
# 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
contrib_wildcards = contrib_wildcard.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)
logger.info("Creating the dataset")
from bpnet.datasets import StrandedProfile, SeqClassification
if fasta_file is not None:
if regions is None:
raise ValueError(
"fasta_file specified. Expecting regions to be specified as well"
)
dl_valid = SeqClassification(
fasta_file=fasta_file,
intervals_file=regions,
incl_chromosomes=include_chr,
excl_chromosomes=exclude_chr,
auto_resize_len=seq_width,
)
chrom_sizes = _chrom_sizes(fasta_file)
else:
if dataspec is None:
logger.info("Using dataspec used to train the model")
# Specify dataspec
dataspec = model_dir / "dataspec.yml"
ds = DataSpec.load(dataspec)
dl_valid = StrandedProfile(ds,
incl_chromosomes=include_chr,
excl_chromosomes=exclude_chr,
intervals_file=regions,
peak_width=peak_width,
shuffle=False,
seq_width=seq_width)
chrom_sizes = _chrom_sizes(ds.fasta_file)
# Setup contribution score trimming (not required currently)
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, contrib_wildcards)
]
logger.info(f"Using the following interpretation targets:")
for n in intp_names:
print(n)
if max_regions is not None:
if len(dl_valid) > max_regions:
logging.info(
f"Using {max_regions} regions instead of the original {len(dl_valid)}"
)
else:
logging.info(
f"--max-regions={max_regions} is larger than the dataset size: {len(dl_valid)}. "
"Using the dataset size for max-regions")
max_regions = len(dl_valid)
else:
max_regions = len(dl_valid)
max_batches = np.ceil(max_regions / batch_size)
writer = HDF5BatchWriter(output_file, chunk_size=storage_chunk_size)
for i, batch in enumerate(
tqdm(dl_valid.batch_iter(batch_size=batch_size,
shuffle=shuffle_regions,
num_workers=num_workers),
total=max_batches)):
# store the original batch containing 'inputs' and 'targets'
if skip_bias:
batch['inputs'] = {
'seq': batch['inputs']['seq']
} # ignore all other inputs
if max_batches > 0:
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_contrib = seqmodel.contrib_score(
batch['inputs']['seq'],
name=name,
method=method,
batch_size=None) # don't second-batch
# put contribution scores to the dictionary
# also trim the contribution scores appropriately so that
# the output will always be w.r.t. the peak center
batch[f"/hyp_contrib/{name}"] = hyp_contrib[:, trim_start:trim_end]
# trim the sequence as well
# Trim the sequence
batch['inputs']['seq'] = batch['inputs']['seq'][:, trim_start:trim_end]
# ? maybe it would it be better to have an explicit ContribFileWriter.
# that way the written schema would be fixed
writer.batch_write(batch)
# add chromosome sizes
writer.f.attrs['chrom_sizes'] = json.dumps(chrom_sizes)
writer.close()
logger.info(f"Done. Contribution score file was saved to: {output_file}")
def bpnet_data_gw(dataspec,
intervals_file=None,
peak_width=200,
seq_width=None,
shuffle=True,
track_transform=None,
total_count_transform=lambda x: np.log(1 + x),
include_metadata=False,
include_classes=False,
tasks=None,
valid_chr=['chr2', 'chr3', 'chr4'],
test_chr=['chr1', 'chr8', 'chr9'],
exclude_chr=[]):
"""Genome-wide bpnet data
"""
# NOTE = only chromosomes from chr1-22 and chrX and chrY are considered here
# (e.g. all other chromosomes like ChrUn... are omitted)
from bpnet.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)
# get the list of all chromosomes from the fasta file
all_chr = _chrom_names(dataspec.fasta_file)
if tasks is None:
tasks = list(dataspec.task_specs)
train = StrandedProfile(dataspec, peak_width,
seq_width=seq_width,
intervals_file=intervals_file,
intervals_format='bed3+labels',
include_metadata=include_metadata,
include_classes=include_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,
track_transform=track_transform,
total_count_transform=total_count_transform)
valid = [('train-valid-genome-wide',
StrandedProfile(dataspec, peak_width,
seq_width=seq_width,
intervals_file=intervals_file,
intervals_format='bed3+labels',
include_metadata=include_metadata,
include_classes=include_classes,
tasks=tasks,
incl_chromosomes=valid_chr,
shuffle=shuffle,
track_transform=track_transform,
total_count_transform=total_count_transform))]
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,
intervals_format='bed3+labels',
include_metadata=include_metadata,
include_classes=True,
tasks=tasks,
incl_chromosomes=valid_chr,
shuffle=shuffle,
track_transform=track_transform,
total_count_transform=total_count_transform))]
# Add also the peak regions
valid = valid + [
('valid-peaks', StrandedProfile(dataspec, peak_width,
seq_width=seq_width,
intervals_file=None,
intervals_format='bed3+labels',
include_metadata=include_metadata,
tasks=tasks,
include_classes=False, # dataspec doesn't contain labels
incl_chromosomes=valid_chr,
shuffle=shuffle,
track_transform=track_transform,
total_count_transform=total_count_transform)),
('train-peaks', StrandedProfile(dataspec, peak_width,
seq_width=seq_width,
intervals_file=None,
intervals_format='bed3+labels',
include_metadata=include_metadata,
tasks=tasks,
include_classes=False, # dataspec doesn't contain labels
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,
track_transform=track_transform,
total_count_transform=total_count_transform)),
# use the default metric for the peak sets
]
return train, valid
def bpnet_data(dataspec,
peak_width=1000,
intervals_file=None,
intervals_format='bed',
seq_width=None,
shuffle=True,
total_count_transform=lambda x: np.log(1 + x),
track_transform=None,
include_metadata=False,
valid_chr=['chr2', 'chr3', 'chr4'],
test_chr=['chr1', 'chr8', 'chr9'],
exclude_chr=[],
augment_interval=True,
interval_augmentation_shift=200,
tasks=None):
"""BPNet default data-loader
Args:
tasks: specify a subset of the tasks to use in the dataspec.yml. If None, all tasks will be specified.
"""
from bpnet.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 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
# get the list of all chromosomes from the fasta file
all_chr = _chrom_names(dataspec.fasta_file)
return (StrandedProfile(dataspec, peak_width,
intervals_file=intervals_file,
intervals_format=intervals_format,
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,
shuffle=shuffle,
track_transform=track_transform,
total_count_transform=total_count_transform,
interval_transformer=interval_transformer),
[('valid-peaks', StrandedProfile(dataspec,
peak_width,
intervals_file=intervals_file,
intervals_format=intervals_format,
seq_width=seq_width,
include_metadata=include_metadata,
incl_chromosomes=valid_chr,
tasks=tasks,
interval_transformer=interval_transformer,
shuffle=shuffle,
track_transform=track_transform,
total_count_transform=total_count_transform)),
('train-peaks', StrandedProfile(dataspec, peak_width,
intervals_file=intervals_file,
intervals_format=intervals_format,
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,
interval_transformer=interval_transformer,
shuffle=shuffle,
track_transform=track_transform,
total_count_transform=total_count_transform)),
])
def __init__(self, ds,
peak_width=200,
seq_width=None,
incl_chromosomes=None,
excl_chromosomes=None,
intervals_file=None,
intervals_format='bed',
include_metadata=True,
tasks=None,
include_classes=False,
shuffle=True,
interval_transformer=None,
track_transform=None,
total_count_transform=lambda x: np.log(1 + x)):
"""Dataset for loading the bigwigs and fastas
Args:
ds (bpnet.dataspecs.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.
intervals_format: interval_file format. Available: bed, bed3, bed3+labels
shuffle: True
track_transform: function to be applied to transform the tracks (shape=(batch, seqlen, channels))
total_count_transform: transform to apply to the total counts
TODO - shall we standardize this to have also the inverse operation?
"""
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
assert intervals_format in ['bed3', 'bed3+labels', 'bed']
self.shuffle = shuffle
self.intervals_file = intervals_file
self.intervals_format = intervals_format
self.incl_chromosomes = incl_chromosomes
self.excl_chromosomes = excl_chromosomes
self.total_count_transform = total_count_transform
self.track_transform = track_transform
self.include_classes = include_classes
# 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
# Load chromosome lengths
self.chrom_lens = _chrom_sizes(self.ds.fasta_file)
if self.intervals_file is None:
# concatenate the bed files
self.dfm = pd.concat([TsvReader(task_spec.peaks,
num_chr=False,
incl_chromosomes=incl_chromosomes,
excl_chromosomes=excl_chromosomes,
chromosome_lens=self.chrom_lens,
resize_width=max(self.peak_width, self.seq_width)
).df.iloc[:, :3].assign(task=task)
for task, task_spec in self.ds.task_specs.items()
if task_spec.peaks is not None])
assert list(self.dfm.columns)[:4] == [0, 1, 2, "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,
# optional
label_dtype=int if self.intervals_format == 'bed3+labels' else None,
mask_ambigous=-1 if self.intervals_format == 'bed3+labels' else None,
# --------------------------------------------
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.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 bpnet_train(dataspec,
output_dir,
premade='bpnet9',
config=None,
override='',
gpu=0,
memfrac_gpu=0.45,
num_workers=8,
vmtouch=False,
in_memory=False,
wandb_project="",
cometml_project="",
run_id=None,
note_params="",
overwrite=False):
"""Train a model using gin-config
Output files:
train.log - log file
model.h5 - Keras model HDF5 file
seqmodel.pkl - Serialized SeqModel. This is the main trained model.
eval-report.ipynb/.html - evaluation report containing training loss curves and some example model predictions.
You can specify your own ipynb using `--override='report_template.name="my-template.ipynb"'`.
model.gin -> copied from the input
dataspec.yaml -> copied from the input
"""
cometml_experiment, wandb_run, output_dir = start_experiment(
output_dir=output_dir,
cometml_project=cometml_project,
wandb_project=wandb_project,
run_id=run_id,
note_params=note_params,
overwrite=overwrite)
# remember the executed command
write_json(
{
"dataspec": dataspec,
"output_dir": output_dir,
"premade": premade,
"config": config,
"override": override,
"gpu": gpu,
"memfrac_gpu": memfrac_gpu,
"num_workers": num_workers,
"vmtouch": vmtouch,
"in_memory": in_memory,
"wandb_project": wandb_project,
"cometml_project": cometml_project,
"run_id": run_id,
"note_params": note_params,
"overwrite": overwrite
},
os.path.join(output_dir, 'bpnet-train.kwargs.json'),
indent=2)
# copy dataspec.yml and input config file over
if config is not None:
shutil.copyfile(config, os.path.join(output_dir, 'input-config.gin'))
# parse and validate the dataspec
ds = DataSpec.load(dataspec)
related_dump_yaml(ds.abspath(), os.path.join(output_dir, 'dataspec.yml'))
if vmtouch:
if shutil.which('vmtouch') is None:
logger.warn(
"vmtouch is currently not installed. "
"--vmtouch disabled. Please install vmtouch to enable it")
else:
# use vmtouch to load all file to memory
ds.touch_all_files()
# --------------------------------------------
# Parse the config file
# import gin.tf
if gpu is not None:
logger.info(f"Using gpu: {gpu}, memory fraction: {memfrac_gpu}")
create_tf_session(gpu, per_process_gpu_memory_fraction=memfrac_gpu)
gin_files = _get_gin_files(premade, config)
# infer differnet hyper-parameters from the dataspec file
if len(ds.bias_specs) > 0:
use_bias = True
if len(ds.bias_specs) > 1:
# TODO - allow multiple bias track
# - split the heads separately
raise ValueError("Only a single bias track is currently supported")
bias = [v for k, v in ds.bias_specs.items()][0]
n_bias_tracks = len(bias.tracks)
else:
use_bias = False
n_bias_tracks = 0
tasks = list(ds.task_specs)
# TODO - handle multiple track widths?
tracks_per_task = [len(v.tracks) for k, v in ds.task_specs.items()][0]
# figure out the right hyper-parameters
dataspec_bindings = [
f'dataspec="{dataspec}"', f'use_bias={use_bias}',
f'n_bias_tracks={n_bias_tracks}', f'tracks_per_task={tracks_per_task}',
f'tasks={tasks}'
]
gin.parse_config_files_and_bindings(
gin_files,
bindings=dataspec_bindings + override.split(";"),
# NOTE: custom files were inserted right after
# ther user's config file and before the `override`
# parameters specified at the command-line
# This allows the user to disable the bias correction
# despite being specified in the config file
skip_unknown=False)
# --------------------------------------------
# Remember the parsed configs
# comet - log environment
if cometml_experiment is not None:
# log other parameters
cometml_experiment.log_parameters(dict(premade=premade,
config=config,
override=override,
gin_files=gin_files,
gpu=gpu),
prefix='cli/')
# wandb - log environment
if wandb_run is not None:
# store general configs
wandb_run.config.update(
dict_prefix_key(dict(premade=premade,
config=config,
override=override,
gin_files=gin_files,
gpu=gpu),
prefix='cli/'))
return train(
output_dir=output_dir,
cometml_experiment=cometml_experiment,
wandb_run=wandb_run,
num_workers=num_workers,
in_memory=in_memory,
# to execute the sub-notebook
memfrac_gpu=memfrac_gpu,
gpu=gpu)
