How to use the kipoi.specs.Author function in kipoi

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github kipoi / kipoiseq / kipoiseq / dataloaders / sequence.py View on Github external
from copy import deepcopy
from kipoi.metadata import GenomicRanges
from kipoi.data import Dataset, kipoi_dataloader
from kipoi_conda.dependencies import Dependencies
from kipoiseq.transforms import ReorderedOneHot
from kipoi.specs import Author
from kipoi_utils.utils import default_kwargs
from kipoiseq.extractors import FastaStringExtractor
from kipoiseq.transforms.functional import resize_interval
from kipoiseq.utils import to_scalar, parse_dtype

# general dependencies
# bioconda::genomelake', TODO - add genomelake again once it gets released with pyfaidx to bioconda
deps = Dependencies(conda=['bioconda::pybedtools', 'bioconda::pyfaidx', 'numpy', 'pandas'],
                    pip=['kipoiseq'])
package_authors = [Author(name='Ziga Avsec', github='avsecz'),
                   Author(name='Roman Kreuzhuber', github='krrome')]

# Object exported on import *
__all__ = ['SeqIntervalDl', 'StringSeqIntervalDl', 'BedDataset']


class BedDataset(object):
    """Reads a tsv file in the following format:
    ```
    chr  start  stop  task1  task2 ...
    ```

    # Arguments
      tsv_file: tsv file type
      bed_columns: number of columns corresponding to the bed file. All the columns
        after that will be parsed as targets
github kipoi / kipoiseq / kipoiseq / dataloaders / splicing.py View on Github external
from kipoi.data import Dataset, kipoi_dataloader
from kipoi.metadata import GenomicRanges
from kipoi.specs import Author, Dependencies
from kipoi.data import SampleIterator

import gffutils
from pyfaidx import Fasta
import pickle

# general dependencies
# bioconda::genomelake', TODO - add genomelake again once it gets released with pyfaidx to bioconda
deps = Dependencies(conda=['bioconda::pyfaidx', 'numpy', 'pandas'],
                    pip=['kipoiseq', 'kipoi'])
package_authors = [Author(name='Jun Cheng', github='s6juncheng')]

__all__ = ['ExonInterval', 'generate_exons', 'MMSpliceDl']

# python 2.7 compatibility

try:
    FileNotFoundError
except NameError:
    FileNotFoundError = IOError

try:
    ModuleNotFoundError
except NameError:
    ModuleNotFoundError = ImportError