boltznet 0.3.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- boltznet/__init__.py +3 -0
- boltznet/_internal/CONFIG.py +51 -0
- boltznet/_internal/aln.py +1323 -0
- boltznet/_internal/base_data_type.py +107 -0
- boltznet/_internal/browser.py +538 -0
- boltznet/_internal/browser_util.py +344 -0
- boltznet/_internal/coverage.py +96 -0
- boltznet/_internal/factory.py +63 -0
- boltznet/_internal/fileDataType.py +332 -0
- boltznet/_internal/genomes.py +304 -0
- boltznet/_internal/model_create.py +1711 -0
- boltznet/_internal/model_disect.py +1190 -0
- boltznet/_internal/model_predict.py +2254 -0
- boltznet/_internal/model_predict_create.py +263 -0
- boltznet/_internal/model_predict_models.py +132 -0
- boltznet/_internal/sequence.py +467 -0
- boltznet/_internal/tf_util.py +2160 -0
- boltznet/_internal/util.py +732 -0
- boltznet/boltznet_tf.py +328 -0
- boltznet/selftest.py +32 -0
- boltznet/test_module.py +14 -0
- boltznet/testdata/__init__.py +0 -0
- boltznet/testdata/ecoli.gff +6447 -0
- boltznet/testdata/promoters.fa +1185 -0
- boltznet-0.3.0.dist-info/METADATA +115 -0
- boltznet-0.3.0.dist-info/RECORD +30 -0
- boltznet-0.3.0.dist-info/WHEEL +5 -0
- boltznet-0.3.0.dist-info/entry_points.txt +3 -0
- boltznet-0.3.0.dist-info/licenses/LICENSE +16 -0
- boltznet-0.3.0.dist-info/top_level.txt +1 -0
boltznet/__init__.py
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Configuration file that can be modified for each user
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Primarily to indicate locations of files etc
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@author: jgalag
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"""
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# SERVER LOCATIONS
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server_data_root = '/Volumes/eng_research_galagan/seqdata/projects/ecoli'
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'''Mounted server location of seqdata/projects/ecoli'''
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server_projects_root = '/Volumes/eng_research_galagan/seqdata/projects/'
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'''Mounted server location of seqdata/projects/'''
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server_meme_root = '%s/downstream_files/analysis/meme' % server_data_root
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'''Mounted server location of meme analysis directory'''
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boltznet_comparison_server='/Volumes/eng_research_galagan/seqdata/projects/boltzNetComparisons/'
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new_regulon_dir='/Volumes/eng_research_galagan/seqdata/projects/ecoli/downstream_files/analysis/known_motifs/Regulon-v12-confirmed'
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'''Location of regulonDB meme file'''
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# LOCAL PLACES
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model_dir = '/Users/jgalag/Dropbox/Python/CNNModels/models'
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'''Location for models'''
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model_json_dir = '%s/json'%model_dir
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'''Location for model json files'''
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bokeh_temp_dir = '/Users/jgalag/Dropbox/Python/CNNModels/bokeh_temp'
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'''Temp dir for browsers'''
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browser_dir = '/Users/jgalag/Dropbox/Python/CNNModels/browsers'
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'''Standard location for TF genome browsers and model browsers'''
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data_dir = '/Users/jgalag/Dropbox/Python/CNNModels/source/datafiles'
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'''Location of datafiles including genome files and geneview files'''
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# figpath='/Users/jgalag/Dropbox/Projects/Papers/Ecoli Papers/Model Paper/resub'
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figpath='/Users/jgalag/Dropbox/Projects/Papers/Ecoli Papers/Boltznet/NatureFormat/Nat Comm Files/Final Submission/figures'
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file_dir = '/Users/jgalag/Dropbox/Python/CNNModels/input_files'
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'''Loction of Files for import and export'''
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source_dir ='/Users/jgalag/Dropbox/Python/CNNModels/source'
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'''Location of source folder'''
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