4.1. datanator package

4.1.1. Subpackages

• 4.1.1.1. datanator.config package
  • 4.1.1.1.1. Submodules
  • 4.1.1.1.2. datanator.config.core module
  • 4.1.1.1.3. Module contents
• 4.1.1.2. datanator.core package
  • 4.1.1.2.1. Submodules
  • 4.1.1.2.2. datanator.core.data_model module
  • 4.1.1.2.3. datanator.core.data_source module
  • 4.1.1.2.4. Module contents
• 4.1.1.3. datanator.data_source package
  • 4.1.1.3.1. Subpackages
    • 4.1.1.3.1.1. datanator.data_source.array_express_tools package
      • 4.1.1.3.1.1.1. Submodules
      • 4.1.1.3.1.1.2. datanator.data_source.array_express_tools.ensembl_tools module
      • 4.1.1.3.1.1.3. Module contents
    • 4.1.1.3.1.2. datanator.data_source.builds package
      • 4.1.1.3.1.2.1. Submodules
      • 4.1.1.3.1.2.2. datanator.data_source.builds.full module
      • 4.1.1.3.1.2.3. datanator.data_source.builds.med module
      • 4.1.1.3.1.2.4. datanator.data_source.builds.test module
      • 4.1.1.3.1.2.5. datanator.data_source.builds.test_log module
      • 4.1.1.3.1.2.6. Module contents
    • 4.1.1.3.1.3. datanator.data_source.process_rna_seq package
      • 4.1.1.3.1.3.1. Submodules
      • 4.1.1.3.1.3.2. datanator.data_source.process_rna_seq.command_line_core module
      • 4.1.1.3.1.3.3. datanator.data_source.process_rna_seq.core module
      • 4.1.1.3.1.3.4. datanator.data_source.process_rna_seq.download_cdna module
      • 4.1.1.3.1.3.5. Module contents
  • 4.1.1.3.2. Submodules
  • 4.1.1.3.3. datanator.data_source.corum_nosql module
  • 4.1.1.3.4. datanator.data_source.ec module
  • 4.1.1.3.5. datanator.data_source.gene_ortholog module
  • 4.1.1.3.6. datanator.data_source.intact_nosql module
  • 4.1.1.3.7. datanator.data_source.kegg_org_code module
  • 4.1.1.3.8. datanator.data_source.kegg_orthology module
  • 4.1.1.3.9. datanator.data_source.kegg_reaction_class module
  • 4.1.1.3.10. datanator.data_source.metabolite_nosql module
  • 4.1.1.3.11. datanator.data_source.metabolites_meta_collection module
  • 4.1.1.3.12. datanator.data_source.modomics module
  • 4.1.1.3.13. datanator.data_source.pax_nosql module
  • 4.1.1.3.14. datanator.data_source.protein_aggregate module
  • 4.1.1.3.15. datanator.data_source.sabio_compound module
  • 4.1.1.3.16. datanator.data_source.sabio_reaction module
  • 4.1.1.3.17. datanator.data_source.sabio_rk module
  • 4.1.1.3.18. datanator.data_source.sabio_rk_json_mongo module
  • 4.1.1.3.19. datanator.data_source.sabio_rk_nosql module
  • 4.1.1.3.20. datanator.data_source.sqlite_to_json module
  • 4.1.1.3.21. datanator.data_source.taxon_tree module
  • 4.1.1.3.22. datanator.data_source.uniprot_nosql module
  • 4.1.1.3.23. Module contents
• 4.1.1.4. datanator.schema_2 package
  • 4.1.1.4.1. Submodules
  • 4.1.1.4.2. datanator.schema_2.migrate_corum module
  • 4.1.1.4.3. datanator.schema_2.migrate_ec module
  • 4.1.1.4.4. datanator.schema_2.migrate_metabolite_concentration module
  • 4.1.1.4.5. datanator.schema_2.migrate_metabolites_meta module
  • 4.1.1.4.6. datanator.schema_2.migrate_taxon_tree module
  • 4.1.1.4.7. datanator.schema_2.migrate_uniprot module
  • 4.1.1.4.8. datanator.schema_2.transform module
  • 4.1.1.4.9. datanator.schema_2.transform_metabolite_concentrations module
  • 4.1.1.4.10. datanator.schema_2.transform_metabolites_meta module
  • 4.1.1.4.11. Module contents
• 4.1.1.5. datanator.util package
  • 4.1.1.5.1. Submodules
  • 4.1.1.5.2. datanator.util.base26 module
  • 4.1.1.5.3. datanator.util.build_util module
  • 4.1.1.5.4. datanator.util.calc_tanimoto module
  • 4.1.1.5.5. datanator.util.chem_util module
  • 4.1.1.5.6. datanator.util.constants module
  • 4.1.1.5.7. datanator.util.file_util module
  • 4.1.1.5.8. datanator.util.index_collection module
  • 4.1.1.5.9. datanator.util.molecule_util module
  • 4.1.1.5.10. datanator.util.mongo_util module
  • 4.1.1.5.11. datanator.util.reaction_util module
  • 4.1.1.5.12. datanator.util.rna_halflife_util module
  • 4.1.1.5.13. datanator.util.rna_seq_util module
  • 4.1.1.5.14. datanator.util.taxonomy_util module
  • 4.1.1.5.15. datanator.util.warning_util module
  • 4.1.1.5.16. Module contents

4.1.2. Submodules

4.1.3. datanator.__main__ module

Command line utilities

Author

Yosef Roth <yosefdroth@gmail.com>

Author

Jonathan Karr <jonrkarr@gmail.com>

Author

Saahith Pochiraju <saahith116@gmail.com>

Date

2017-04-12

Copyright

2017, Karr Lab

License

MIT

class datanator.__main__.AggregateBuildController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['--path'], {'type': <class 'str'>, 'default': '/root/.wc/data/datanator', 'help': 'path to build the database'}), (['--verbose'], {'type': <class 'bool'>, 'default': False, 'help': 'verbosity'}), (['--max-entries'], {'type': <class 'int'>, 'default': inf, 'help': 'number of normalized entries to add per database. Default: Full Database'}), (['--build-on-existing'], {'type': <class 'bool'>, 'default': False, 'help': 'load from existing database on karr lab server'}), (['--load-full-small-dbs'], {'type': <class 'bool'>, 'default': True, 'help': 'loads entire small database modules'})]

description = 'Builds Aggregated Database'

help = 'Builds Aggregated Database'

label = 'aggregate'

stacked_on = 'build'

stacked_type = 'nested'

class datanator.__main__.App(label=None, **kw)

Bases: cement.core.foundation.App

class Meta

Bases: object

base_controller = 'base'

handlers = [<class 'datanator.__main__.BaseController'>, <class 'datanator.__main__.UploadDataController'>, <class 'datanator.__main__.UploadReferenceGenome'>, <class 'datanator.__main__.UploadRNASeqExperiment'>, <class 'datanator.__main__.UploadData'>, <class 'datanator.__main__.DownloadController'>, <class 'datanator.__main__.BuildController'>, <class 'datanator.__main__.AggregateBuildController'>, <class 'datanator.__main__.GenerateTemplateController'>, <class 'datanator.__main__.GenerateRNASeqTemplate'>, <class 'datanator.__main__.TaxonomyController'>, <class 'datanator.__main__.TaxonomyGetRankController'>, <class 'datanator.__main__.TaxonomyGetParentsController'>, <class 'datanator.__main__.TaxonomyGetCommonAncestorController'>, <class 'datanator.__main__.TaxonomyGetDistanceToCommonAncestorController'>, <class 'datanator.__main__.TaxonomyGetDistanceToRoot'>, <class 'datanator.__main__.MoleculeController'>, <class 'datanator.__main__.MoleculeGetStructureController'>, <class 'datanator.__main__.MoleculeConvertStructureController'>, <class 'datanator.__main__.ReactionController'>, <class 'datanator.__main__.ReactionGetEcNumberController'>]

label = 'datanator'

class datanator.__main__.BaseController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['-v', '--version'], {'action': 'version', 'version': '0.2'})]

description = 'Utilities for aggregating data for biochemical models'

help = 'Utilities for aggregating data for biochemical models'

label = 'base'

class datanator.__main__.BuildController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['--max-entries'], {'type': <class 'int'>, 'default': inf, 'help': 'number of normalized entries to add per database. Default: Full Database'}), (['--path'], {'type': <class 'str'>, 'default': '/root/.wc/data/datanator', 'help': 'path to build the database'}), (['--clear-existing-content'], {'type': <class 'bool'>, 'default': False, 'help': 'clears existing content of the db if exists'}), (['--verbose'], {'type': <class 'bool'>, 'default': False, 'help': 'verbosity'})]

description = 'Build aggregated database'

help = 'Build aggregated database'

label = 'build'

stacked_on = 'base'

stacked_type = 'nested'

array_express()

corum()

ecmdb()

intact()

jaspar()

pax()

sabio()

uniprot()

class datanator.__main__.DownloadController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['--path'], {'type': <class 'str'>, 'help': 'path to download the modules', 'default': '/root/.wc/data/datanator'})]

description = 'Download existing databases from Karr Lab Server'

help = 'Download existing databases from Karr Lab Server'

label = 'download'

stacked_on = 'base'

stacked_type = 'nested'

aggregate()

array_express()

corum()

ecmdb()

intact()

jaspar()

pax()

sabio()

uniprot()

class datanator.__main__.GenerateRNASeqTemplate(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['directory_name'], {'type': <class 'str'>, 'help': 'path to save the directory'})]

description = 'Generate a folder with excel tables to upload rna-seq experiments'

help = 'Generate a folder with excel tables to upload rna-seq experiments'

label = 'generate-rna-seq-template'

stacked_on = 'base'

stacked_type = 'nested'

class datanator.__main__.GenerateTemplateController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['filename'], {'type': <class 'str'>, 'help': 'path to save the Excel template'})]

description = 'Generate an Excel template for specifying which reactions to aggregate kinetic data about'

help = 'Generate an Excel template for specifying which reactions to aggregate kinetic data about'

label = 'generate-template'

stacked_on = 'base'

stacked_type = 'nested'

class datanator.__main__.MoleculeController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = []

description = 'Molecule utilities'

help = 'Molecule utilities'

label = 'molecule'

stacked_on = 'base'

stacked_type = 'nested'

class datanator.__main__.MoleculeConvertStructureController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['structure'], {'type': <class 'str'>, 'help': 'Structure in InChI, MOL, or canonical SMILES format'}), (['format'], {'type': <class 'str'>, 'help': 'Output format: inchi (InChI), mol (MOL), or can (canonical SMILES)'})]

description = 'Convert molecule structure'

help = 'Convert molecule structure'

label = 'convert-structure'

stacked_on = 'molecule'

stacked_type = 'nested'

class datanator.__main__.MoleculeGetStructureController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['--by-name'], {'dest': 'by_name', 'action': 'store_true', 'default': True, 'help': 'If set, lookup structure by name'}), (['--by-id'], {'dest': 'by_name', 'action': 'store_false', 'default': True, 'help': 'If set, lookup structure by id'}), (['--namespace'], {'type': <class 'str'>, 'help': 'Namespace of id'}), (['name_or_id'], {'type': <class 'str'>, 'help': 'Name or id of the molecule'})]

description = 'Get the structure of a molecule by its name or id'

help = 'Get the structure of a molecule by its name or id'

label = 'get-structure'

stacked_on = 'molecule'

stacked_type = 'nested'

class datanator.__main__.ReactionController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = []

description = 'Reaction utilities'

help = 'Reaction utilities'

label = 'reaction'

stacked_on = 'base'

stacked_type = 'nested'

class datanator.__main__.ReactionGetEcNumberController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['--do-not-restore-data'], {'dest': 'restore_data', 'action': 'store_false', 'help': 'If set, do not restore the data'}), (['--restore-schema'], {'dest': 'restore_schema', 'action': 'store_true', 'help': 'If set, restore the schema'}), (['--do-not-exit-on-error'], {'dest': 'exit_on_error', 'action': 'store_false', 'help': 'If set, do not exit on errors'})]

description = 'Restore the content of the Datanator database'

help = 'Restore the content of the Datanator database'

label = 'restore'

stacked_on = 'db'

stacked_type = 'nested'

class datanator.__main__.TaxonomyController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = []

description = 'Taxonomy utilities'

help = 'Taxonomy utilities'

label = 'taxonomy'

stacked_on = 'base'

stacked_type = 'nested'

class datanator.__main__.TaxonomyGetCommonAncestorController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['taxon_id_or_name_1'], {'type': <class 'str'>, 'help': "Taxon id or name (examples: 9606, 'Homo sapiens')"}), (['taxon_id_or_name_2'], {'type': <class 'str'>, 'help': "Taxon id or name (examples: 9606, 'Homo sapiens')"})]

description = 'Get the latest common ancestor between two taxa'

help = 'Get the latest common ancestor between two taxa'

label = 'get-common-ancestor'

stacked_on = 'taxonomy'

stacked_type = 'nested'

class datanator.__main__.TaxonomyGetDistanceToCommonAncestorController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['taxon_id_or_name_1'], {'type': <class 'str'>, 'help': "Taxon id or name (examples: 9606, 'Homo sapiens')"}), (['taxon_id_or_name_2'], {'type': <class 'str'>, 'help': "Taxon id or name (examples: 9606, 'Homo sapiens')"})]

description = 'Get the distance to the latest common ancestor between two taxa'

help = 'Get the distance to the latest common ancestor between two taxa'

label = 'get-distance-to-common-ancestor'

stacked_on = 'taxonomy'

stacked_type = 'nested'

class datanator.__main__.TaxonomyGetDistanceToRoot(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['taxon_id_or_name'], {'type': <class 'str'>, 'help': "Taxon id or name (examples: 9606, 'Homo sapiens')"})]

description = 'Get the distance to from a taxon to the root of the taxonomic tree'

help = 'Get the distance to from a taxon to the root of the taxonomic tree'

label = 'get-distance-to-root'

stacked_on = 'taxonomy'

stacked_type = 'nested'

class datanator.__main__.TaxonomyGetParentsController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['taxon_id_or_name'], {'type': <class 'str'>, 'help': "Taxon id or name (examples: 9606, 'Homo sapiens')"})]

description = 'Get the parents of a taxon'

help = 'Get the parents of a taxon'

label = 'get-parents'

stacked_on = 'taxonomy'

stacked_type = 'nested'

class datanator.__main__.TaxonomyGetRankController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['taxon_id_or_name'], {'type': <class 'str'>, 'help': "Taxon id or name (examples: 9606, 'Homo sapiens')"})]

description = 'Get the rank of a taxon'

help = 'Get the rank of a taxon'

label = 'get-rank'

stacked_on = 'taxonomy'

stacked_type = 'nested'

class datanator.__main__.UploadData(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['data_type'], {'type': <class 'str'>, 'help': 'type of data to be uploaded'})]

description = 'Upload data from overall schema'

help = 'Upload data from overall schema'

label = 'general-data'

stacked_on = 'upload'

stacked_type = 'nested'

class datanator.__main__.UploadDataController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = []

description = 'Upload reference genome into Datanator. The reference genome must be in Genbank or Ensembl format'

help = 'Upload reference genome into Datanator. The reference genome must be in Genbank or Ensembl format'

label = 'upload'

stacked_on = 'base'

stacked_type = 'nested'

class datanator.__main__.UploadRNASeqExperiment(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['ref-genome-path'], {'type': <class 'str'>, 'help': 'path to reference genome', 'default': '/root/.wc/data/datanator'}), (['--db-path'], {'type': <class 'str'>, 'help': 'path to build the database', 'default': '/root/.wc/data/datanator'})]

description = 'Upload an RNA-seq experiment'

help = 'Upload an RNA-seq experiment'

label = 'rna-seq-experiment'

stacked_on = 'upload'

stacked_type = 'nested'

class datanator.__main__.UploadReferenceGenome(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

class Meta

Bases: object

arguments = [(['genome_path'], {'type': <class 'str'>, 'help': 'path to reference genome', 'default': '/root/.wc/data/datanator'}), (['--db-path'], {'type': <class 'str'>, 'help': 'path to build the database', 'default': '/root/.wc/data/datanator'})]

description = 'Upload a ref-seq genome'

help = 'Upload a ref-seq genome'

label = 'reference-genome'

stacked_on = 'upload'

stacked_type = 'nested'

datanator.__main__.create_taxon(id_or_name)

Create a taxon with NCBI id=:obj:id_or_name or name=:obj:id_or_name

Parameters

id_or_name (str) – NCBI id or name

Returns

taxon

Return type

taxonomy_util.Taxon

datanator.__main__.main()

4.1.4. datanator._version module

4.1.5. datanator.parse_metabolite_concentration module

class datanator.parse_metabolite_concentration.ParseMetaboliteConcentration(MongoDB=None, db=None, collection=None, max_entries=inf, username=None, password=None, authSource='admin', readPreference='nearest')

Bases: datanator_query_python.util.mongo_util.MongoUtil

parse_metabolite()

Read JSON metabolite concentration files from Github and insert separate documents for each metabolite into MongoDB database

Parameters

() –

Returns

()

datanator.parse_metabolite_concentration.main()

4.1.6. Module contents