4.1. datanator package¶
4.1.1. Subpackages¶
- 4.1.1.1. datanator.api package
- 4.1.1.1.1. Subpackages
- 4.1.1.1.1.1. datanator.api.lib package
- 4.1.1.1.1.1.1. Subpackages
- 4.1.1.1.1.1.1.1. datanator.api.lib.complex package
- 4.1.1.1.1.1.1.2. datanator.api.lib.filter package
- 4.1.1.1.1.1.1.3. datanator.api.lib.metabolite package
- 4.1.1.1.1.1.1.4. datanator.api.lib.reaction package
- 4.1.1.1.1.1.1.5. datanator.api.lib.search package
- 4.1.1.1.1.1.1.6. datanator.api.lib.subunit package
- 4.1.1.1.1.1.2. Submodules
- 4.1.1.1.1.1.3. datanator.api.lib.data_manager module
- 4.1.1.1.1.1.4. Module contents
- 4.1.1.1.1.1.1. Subpackages
- 4.1.1.1.1.2. datanator.api.query package
- 4.1.1.1.1.2.1. Submodules
- 4.1.1.1.1.2.2. datanator.api.query.dna_protein_interactions module
- 4.1.1.1.1.2.3. datanator.api.query.metabolite_concentrations module
- 4.1.1.1.1.2.4. datanator.api.query.protein_abundance module
- 4.1.1.1.1.2.5. datanator.api.query.protein_protein_interactions module
- 4.1.1.1.1.2.6. datanator.api.query.reaction_kinetics module
- 4.1.1.1.1.2.7. datanator.api.query.text_search module
- 4.1.1.1.1.2.8. Module contents
- 4.1.1.1.1.1. datanator.api.lib package
- 4.1.1.1.2. Submodules
- 4.1.1.1.3. datanator.api.serializer module
- 4.1.1.1.4. datanator.api.urls module
- 4.1.1.1.5. datanator.api.views module
- 4.1.1.1.6. Module contents
- 4.1.1.1.1. Subpackages
- 4.1.1.2. datanator.builds package
- 4.1.1.3. datanator.config package
- 4.1.1.4. datanator.core package
- 4.1.1.4.1. Subpackages
- 4.1.1.4.2. Submodules
- 4.1.1.4.3. datanator.core.common_schema module
- 4.1.1.4.4. datanator.core.data_model module
- 4.1.1.4.5. datanator.core.data_query module
- 4.1.1.4.6. datanator.core.data_source module
- 4.1.1.4.7. datanator.core.json_schema module
- 4.1.1.4.8. datanator.core.models module
- 4.1.1.4.9. datanator.core.query_nosql module
- 4.1.1.4.10. datanator.core.upload_data module
- 4.1.1.4.11. Module contents
- 4.1.1.5. datanator.data_source package
- 4.1.1.5.1. Subpackages
- 4.1.1.5.2. Submodules
- 4.1.1.5.3. datanator.data_source.array_express module
- 4.1.1.5.4. datanator.data_source.bio_portal module
- 4.1.1.5.5. datanator.data_source.corum module
- 4.1.1.5.6. datanator.data_source.corum_nosql module
- 4.1.1.5.7. datanator.data_source.cron_aggregate module
- 4.1.1.5.8. datanator.data_source.ecmdb module
- 4.1.1.5.9. datanator.data_source.ensembl module
- 4.1.1.5.10. datanator.data_source.ezyme module
- 4.1.1.5.11. datanator.data_source.intact module
- 4.1.1.5.12. datanator.data_source.intact_nosql module
- 4.1.1.5.13. datanator.data_source.jaspar module
- 4.1.1.5.14. datanator.data_source.kegg module
- 4.1.1.5.15. datanator.data_source.kegg_orthology module
- 4.1.1.5.16. datanator.data_source.kegg_reaction_class module
- 4.1.1.5.17. datanator.data_source.metabolite_nosql module
- 4.1.1.5.18. datanator.data_source.metabolites_meta_collection module
- 4.1.1.5.19. datanator.data_source.pax module
- 4.1.1.5.20. datanator.data_source.pax_nosql module
- 4.1.1.5.21. datanator.data_source.refseq module
- 4.1.1.5.22. datanator.data_source.sabio_rk module
- 4.1.1.5.23. datanator.data_source.sabio_rk_nosql module
- 4.1.1.5.24. datanator.data_source.sqlite_to_json module
- 4.1.1.5.25. datanator.data_source.taxon_tree module
- 4.1.1.5.26. datanator.data_source.uniprot module
- 4.1.1.5.27. datanator.data_source.uniprot_nosql module
- 4.1.1.5.28. Module contents
- 4.1.1.6. datanator.rest package
- 4.1.1.7. datanator.util package
- 4.1.1.7.1. Submodules
- 4.1.1.7.2. datanator.util.build_util module
- 4.1.1.7.3. datanator.util.calc_tanimoto module
- 4.1.1.7.4. datanator.util.chem_util module
- 4.1.1.7.5. datanator.util.constants module
- 4.1.1.7.6. datanator.util.file_util module
- 4.1.1.7.7. datanator.util.index_collection module
- 4.1.1.7.8. datanator.util.molecule_util module
- 4.1.1.7.9. datanator.util.mongo_util module
- 4.1.1.7.10. datanator.util.reaction_util module
- 4.1.1.7.11. datanator.util.rna_seq_util module
- 4.1.1.7.12. datanator.util.server_util module
- 4.1.1.7.13. datanator.util.standardize_util module
- 4.1.1.7.14. datanator.util.taxonomy_util module
- 4.1.1.7.15. datanator.util.warning_util module
- 4.1.1.7.16. 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)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
Meta
[source]¶ 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'})][source]¶
-
-
class
-
class
datanator.__main__.
App
(label=None, **kw)[source]¶ Bases:
cement.core.foundation.App
-
class
Meta
[source]¶ Bases:
object
-
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__.GetDataController'>, <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'>, <class 'datanator.__main__.DbController'>, <class 'datanator.__main__.DbRestoreController'>][source]¶
-
-
class
-
class
datanator.__main__.
BaseController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
BuildController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
Meta
[source]¶ 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'})][source]¶
-
-
class
-
class
datanator.__main__.
DbController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
DbRestoreController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
Meta
[source]¶ 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'})][source]¶
-
-
class
-
class
datanator.__main__.
DownloadController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
GenerateRNASeqTemplate
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
GenerateTemplateController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
Meta
[source]¶ Bases:
object
-
arguments
= [(['filename'], {'type': <class 'str'>, 'help': 'path to save the Excel template'})][source]¶
-
description
= 'Generate an Excel template for specifying which reactions to aggregate kinetic data about'[source]¶
-
-
class
-
class
datanator.__main__.
GetDataController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
Meta
[source]¶ Bases:
object
-
arguments
= [(['input_file'], {'type': <class 'str'>, 'help': 'path to the input data spreadsheet (.xlsx)'}), (['output_file'], {'type': <class 'str'>, 'help': 'path to the output data spreadsheet (.xlsx)'}), (['--max-taxon-dist'], {'help': 'Maximum acceptable taxonomic distance', 'type': <class 'int'>, 'default': None}), (['--taxon-dist-scale'], {'help': 'Exponential constant for scoring taxonomic distance', 'type': <class 'float'>, 'default': nan}), (['--include-variants'], {'help': 'If set, include data from genetic variants', 'action': 'store_true', 'default': False}), (['--temperature'], {'help': 'Target temperature', 'type': <class 'float'>, 'default': 37.0}), (['--temperature-std'], {'help': 'Standard deviation for scoring temperatures', 'type': <class 'float'>, 'default': 1.0}), (['--ph'], {'help': 'Target pH', 'type': <class 'float'>, 'default': 7.5}), (['--ph-std'], {'help': 'Standard deviation for scoring pHs', 'type': <class 'float'>, 'default': 0.3})][source]¶
-
-
class
-
class
datanator.__main__.
MoleculeController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
MoleculeConvertStructureController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
MoleculeGetStructureController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
Meta
[source]¶ 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'})][source]¶
-
-
class
-
class
datanator.__main__.
ReactionController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
ReactionGetEcNumberController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
Meta
[source]¶ Bases:
object
-
class
-
class
datanator.__main__.
TaxonomyController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
TaxonomyGetCommonAncestorController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
TaxonomyGetDistanceToCommonAncestorController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
TaxonomyGetDistanceToRoot
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
TaxonomyGetParentsController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
TaxonomyGetRankController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
UploadData
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
UploadDataController
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
UploadRNASeqExperiment
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
-
class
datanator.__main__.
UploadReferenceGenome
(*args, **kw)[source]¶ Bases:
cement.ext.ext_argparse.ArgparseController
4.1.4. datanator.datanator module¶
Author: | Yosef Roth <yosefdroth@gmail.com> |
---|---|
Author: | Jonathan Karr <jonrkarr@gmail.com> |
Date: | 2017-04-06 |
Copyright: | 2017, Karr Lab |
License: | MIT |
-
class
datanator.datanator.
Datanator
(max_taxon_dist=None, include_variants=False, min_temp=None, max_temp=None, min_ph=None, max_ph=None)[source]¶ Bases:
object
4.1.5. datanator.io module¶
Utilities for reading and writing data to/from files
Author: | Yosef Roth <yosefdroth@gmail.com> |
---|---|
Author: | Jonathan Karr <jonrkarr@gmail.com> |
Date: | 2017-04-14 |
Copyright: | 2017, Karr Lab |
License: | MIT |
-
class
datanator.io.
InputReader
[source]¶ Bases:
object
-
parse_reaction_equation
(equation, compartments, species)[source]¶ Parse a reaction equation, e.g.
- [c]: ATP + H2O ==> ADP + PI + H
- GLC[e] + ATP[c] + H2O[c] ==> GLC[c] + ADP[c] + PI[c] + H[c]
Parameters: - equation (
str
) – reaction equation - compartments (
list
ofdata_model.Compartment
) – list of compartments - species (
list
ofdata_model.Specie
) – list of species
Returns: reaction
Return type: data_model.Reaction
-
read_compartments
(ws)[source]¶ Read compartments from an Excel worksheet
Parameters: ws ( openpyxl.Worksheet
) – worksheetReturns: list of compartments Return type: list
ofdata_model.Compartment
-
read_genetics
(ws)[source]¶ Read taxon from an Excel worksheet
Parameters: ws ( openpyxl.Worksheet
) – worksheetReturns: taxon Return type: data_model.Genetics
-
read_reactions
(ws, compartments, species)[source]¶ Read reactions from an Excel worksheet
Parameters: - ws (
openpyxl.Worksheet
) – worksheet - compartments (
list
ofdata_model.Compartment
) – list of compartments - species (
list
ofdata_model.Specie
) – list of species
Returns: list of reactions
Return type: list
ofdata_model.Reaction
- ws (
-
read_species
(ws)[source]¶ Read species from an Excel worksheet
Parameters: ws ( openpyxl.Worksheet
) – worksheetReturns: list of species Return type: list
ofdata_model.Specie
-
run
(filename)[source]¶ Read input data from an Excel workbook
Parameters: filename ( str
) – filename of Excel workbookReturns: data_model.Genetics
: geneticslist
ofdata_model.Compartment
: list of compartmentslist
ofdata_model.Specie
: list of specieslist
ofdata_model.Reaction
: list of reactions
Return type: tuple
-
-
class
datanator.io.
ResultsWriter
[source]¶ Bases:
object
Save reaction kinetic data to an Excel workbook
-
classmethod
run
(taxon, reactions, filename)[source]¶ Save a list of reaction kinetic data to an Excel workbook or set of csv/tsv files
Parameters: - taxon (
str
) – taxon - reactions (
list
ofdatanator.datanator.SabioResult
) – list of reactions and their kinetic data - filename (
str
) – filename to store the list reaction kinetic data
- taxon (
-
classmethod
run2
(taxon, reactions, filename)[source]¶ Save a list of reaction kinetic data to an Excel workbook or set of csv/tsv files
Parameters: - taxon (
str
) – taxon name - reactions (
list
ofdatanator.datanator.SabioResult
) – list of reactions and their kinetic data - filename (
str
) – filename to store the list reaction kinetic data
- taxon (
-
classmethod