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Allowed pipeline (bias and train) to use defined +/- shifts #259

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Allowed pipeline (bias and train) to use defined +/- shifts #259

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a6f3169
Enable plus/minus shift setting during training
PauBadiaM Sep 17, 2025
5addd21
Remove hardcoding of +/- shifts to None
PauBadiaM Sep 17, 2025
db1a70d
BUmped version
PauBadiaM Sep 17, 2025
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4 changes: 2 additions & 2 deletions chrombpnet/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,8 +57,8 @@ def general_training_args(required_train, optional_train):
required_train.add_argument("-fl", "--chr-fold-path", type=str, required=True, help="Fold information - dictionary with test,valid and train keys and values with corresponding chromosomes")

optional_train.add_argument("-oth", "--outlier-threshold", type=float, default=0.9999, help="threshold to use to filter outlies")
#optional_train.add_argument('-ps', '--plus-shift', type=int, default=None, help="Plus strand shift applied to reads. Estimated if not specified")
#optional_train.add_argument('-ms', '--minus-shift', type=int, default=None, help="Minus strand shift applied to reads. Estimated if not specified")
optional_train.add_argument('-ps', '--plus-shift', type=int, default=None, help="Plus strand shift applied to reads. Estimated if not specified")
optional_train.add_argument('-ms', '--minus-shift', type=int, default=None, help="Minus strand shift applied to reads. Estimated if not specified")
optional_train.add_argument('--ATAC-ref-path', type=str, default=None, help="Path to ATAC reference motifs (ATAC.ref.motifs.txt used by default)")
optional_train.add_argument('--DNASE-ref-path', type=str, default=None, help="Path to DNASE reference motifs (DNASE.ref.motifs.txt used by default)")
optional_train.add_argument('--num-samples', type=int, default=10000, help="Number of reads to sample from BAM/fragment/tagAlign file for shift estimation")
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4 changes: 0 additions & 4 deletions chrombpnet/pipelines.py
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Expand Up @@ -16,8 +16,6 @@ def chrombpnet_train_pipeline(args):
# Shift bam and convert to bigwig
import chrombpnet.helpers.preprocessing.reads_to_bigwig as reads_to_bigwig
args.output_prefix = os.path.join(args.output_dir,"auxiliary/{}data".format(fpx))
args.plus_shift = None
args.minus_shift = None
reads_to_bigwig.main(args)

# QC bigwig
Expand Down Expand Up @@ -273,8 +271,6 @@ def train_bias_pipeline(args):
# Shift bam and convert to bigwig
import chrombpnet.helpers.preprocessing.reads_to_bigwig as reads_to_bigwig
args.output_prefix = os.path.join(args.output_dir,"auxiliary/{}data".format(fpx))
args.plus_shift = None
args.minus_shift = None
reads_to_bigwig.main(args)

# QC bigwig
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -14,7 +14,7 @@
'include_package_data': True,
'description': 'chrombpnet predicts chromatin accessibility from sequence',
'download_url': 'https://github.com/kundajelab/chrombpnet',
'version': '1.0.1',
'version': '1.0.2',
'packages': find_packages(),
'python_requires': '>=3.8',
'install_requires': install_requires,
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