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Alexis Morrissey
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Updating dependencies
1 parent d553be8 commit daa6f6d

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‎Allo/__init__.py‎

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from . import predictPeak
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from . import allocation
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__version__ = '1.1.0'
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__version__ = '1.1.2'

‎Allo/allo‎

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#Arguments
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import argparse
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parser = argparse.ArgumentParser(prog = 'Allo', \
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description = 'Allo is a software that allocates multi-mapped reads in ChIP-seq data\n' \
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'Developed by Alexis Morrissey, Mahony Laboratory @ The Pennsylvania State University', \
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version = "1.1.2"
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parser = argparse.ArgumentParser(prog = 'allo', \
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description = '(Version ' + version + ') Allo is a software that allocates multi-mapped reads in gene regulatory data.\n' \
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'Developed by Mahony Laboratory @ The Pennsylvania State University', \
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epilog= 'For more pre-processing info and basic usage, please visit https://github.com/seqcode/allo')
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parser.add_argument('-v', '--version', action='version', version=version)
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parser.add_argument('input')
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parser.add_argument('-seq', type=str, nargs=1, help='Single-end or paired-end sequencing mode', \
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choices=['pe','se'], required=True, dest='seq')
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choices=['pe','se'], dest='seq', required=True)
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parser.add_argument('-o', type=str, nargs=1, help='Output file name', dest='outfile', default=None)
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parser.add_argument('--mixed', help='Use CNN trained on a dataset with mixed ChIP-seq peaks, narrow by default', action='store_true', default=None)
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parser.add_argument('--dnase', help='Use CNN trained on a DNa-seq datasets', action='store_true', default=None)
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parser.add_argument('--dnase', help='Use CNN trained on a DNase-seq datasets', action='store_true', default=None)
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parser.add_argument('--atac', help='Use CNN trained on a ATAC-seq datasets', action='store_true', default=None)
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parser.add_argument('--splice', help='Remove splice sites based on cigar string when constructing image', action='store_true', default=None)
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parser.add_argument('-p', type=int, nargs=1, help='Number of processes, 1 by default', dest='processes', default=None)
@@ -24,7 +26,7 @@ parser.add_argument('--r2', help='Use read 2 for allocation procedure instead of
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parser.add_argument('--readcount', help='CNN will not be used in allocation, only read counts', action='store_true', default=None)
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parser.add_argument('--random', help='Reads will be randomly assigned (similar to Bowtie and BWA on default)', action='store_true', default=None)
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parser.add_argument('--ignore', help='Ignore warnings about read sorting', action='store_true', default=None)
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parser.add_argument('--parser', help='Ignore warnings about read sorting', action='store_true', default=None)
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parser.add_argument('--parser', help='Parse alignment files to extract uniquely and multi-mapped reads', action='store_true', default=None)
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args = parser.parse_args()
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#Imports
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##Main Method##
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if __name__ == '__main__':
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print("\nRunning Allo version 1.1\n\n")
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print("\nRunning Allo version " + version + "\n\n")
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#Make a folder to store all temp files in allo
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ids = str(randint(0, 10000))
@@ -110,6 +113,9 @@ if __name__ == '__main__':
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seq = 1
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elif args.seq[0] == "pe":
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seq = 0
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else:
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print("Unknown or missing sequencing type: " + seq)
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sys.exit(0)
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#Options for probabilities
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if args.readcount is not None:
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rc = 1

‎setup.py‎

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setup(
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name='bio-allo',
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version='1.1.1',
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version='1.1.2',
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author='Alexis Morrissey',
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author_email='[email protected]',
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packages=['Allo'],
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python_requires='>=3.10',
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scripts=['Allo/allo'],
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url='https://github.com/seqcode/allo/archive/refs/tags/1.1.1.tar.gz',
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url='https://github.com/seqcode/allo/archive/refs/tags/1.1.2.tar.gz',
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license='LICENSE.txt',
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description='A multi-mapped read rescue strategy for ChIP-seq data',
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description='A multi-mapped read rescue strategy for gene regulatory data',
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include_package_data = True,
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install_requires=[
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'numpy',
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'joblib',
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'tensorflow >= 2.11',
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'tensorflow>=2.11,<=2.14',
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'pysam'
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]
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)

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