bioclients 0.2.33__tar.gz

bioclients-0.2.33/LICENSE

@@ -0,0 +1,121 @@
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bioclients-0.2.33/PKG-INFO

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+Metadata-Version: 2.1
+Name: bioclients
+Version: 0.2.33
+Summary: Clients and tools for online biomedical resources, usually via REST APIs.
+Home-page: https://github.com/jeremyjyang/bioclients
+Author: Jeremy Yang
+Author-email: jeremyjyang@gmail.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# `bioclients` <img align="right" src="doc/images/bioclients.png" height="120" alt="bioclients logo">
+
+Python package for access to online biomedical resources,
+usually via REST APIs. Modules generally include
+`Client.py` for command-line use and `Utils.py` for
+integration into other code. With the advent of HTTP web services,
+first SOAP/XML and then mostly REST/JSON, many online APIs
+require very similar methods for data search, requests
+and transforms into usable formats, often TSV.
+
+## Availability and installation
+
+### Installing from PyPI
+
+Releases at <https://pypi.org/project/bioclients/>.
+
+```
+pip3 install bioclients
+```
+However, current development snapshot may included additional functionality.
+
+### Installing from source
+
+Source at <https://github.com/jeremyjyang/bioclients>
+
+___(First download or clone.)___
+
+
+Install `build` package.
+
+```
+python3 -m pip install --upgrade build
+```
+
+Install using `build`.  This supercedes the deprecated `setup.py install` and `easy_install` methods.
+
+```
+cd bioclients
+python3 -m build
+```
+
+## Dependencies
+
+* Python 3.10+
+* Python packages: `pandas`, `requests`, `yaml`, `psycopg2`, `tqdm`, etc. (See [conda/environment.yml](conda/environment.yml)).
+
+## Modules
+
+ [__Allen__](doc/allen.md) &#8226; [__AMP-T2D__](doc/amp__t2d.md) &#8226; [__Badapple__](doc/badapple.md) &#8226; [__BindingDb__](doc/bindingdb.md) &#8226; [__BioGrid__](doc/biogrid.md) &#8226; [__BiomarkerKB__](doc/biomarkerkb.md) &#8226; [__Bioregistry__](doc/bioregistry.md) &#8226; [__BRENDA__](doc/brenda.md) &#8226; [__CAS__](doc/cas.md) &#8226; [__CDC__](doc/cdc.md) &#8226; [__CFDE__](doc/cfde.md) &#8226; [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) &#8226; [__ChEBI__](doc/chebi.md) &#8226; [__ChEMBL__](doc/chembl.md) &#8226; [__ChemIdPlus__](doc/chemidplus.md) &#8226; [__ClinicalTrials.gov__](doc/clinicaltrials.md) &#8226; [__Disease Ontology__](doc/diseaseontology.md) &#8226; [__DisGeNet__](doc/disgenet.md) &#8226; [__DNorm__](doc/dnorm.md) &#8226; [__DrugCentral__](doc/drugcentral.md) &#8226; [__EMBL-EBI__](doc/emblebi.md) &#8226; [__EnsEMBL__](doc/ensembl.md) &#8226; [__Entrez__](doc/entrez.md) &#8226; [__FDA__](doc/fda.md) &#8226; [__Gene Ontology__](doc/geneontology.md) &#8226; [__GTEx__](doc/gtex.md) &#8226; [__GWAS Catalog__](doc/gwascatalog.md) &#8226; [__HUGO__](doc/hugo.md) &#8226; [__HumanBase__](doc/humanbase.md) &#8226; [__iCite__](doc/icite.md) &#8226; [__IDG__](doc/idg.md) &#8226; [__JensenLab__](doc/jensenlab.md) &#8226; [__LINCS__](doc/lincs.md) &#8226; [__MaayanLab__](doc/maayanlab.md) &#8226; [__Medline__](doc/medline.md) &#8226; [__MeSH__](doc/mesh.md) &#8226; [__MONARCH__](doc/monarch.md) &#8226; [__MyGene__](doc/mygene.md) &#8226; [__NCBO__](doc/ncbo.md) &#8226; [__NCATS__](doc/ncats.md) &#8226; [__OMIM__](doc/omim.md) &#8226; [__OncoTree__](doc/oncotree.md) &#8226; [__Open Targets__](doc/opentargets.md) &#8226; [__Panther__](doc/panther.md) &#8226; [__PDB__](doc/pdb.md) &#8226; [__PubChem__](doc/pubchem.md) &#8226; [__PubMed__](doc/pubmed.md) &#8226; [__PubTator__](doc/pubtator.md) &#8226; [__Reactome__](doc/reactome.md) &#8226; [__RXNorm__](doc/rxnorm.md) &#8226; [__STRINGDB__](doc/stringdb.md) &#8226; [__TCGA__](doc/tcga.md) &#8226; [__TINX__](doc/tinx.md) &#8226; [__UBKG__](doc/ubkg.md) &#8226; [__UMLS__](doc/umls.md) &#8226; [__UniProt__](doc/uniprot.md) &#8226; [__Wikidata__](doc/wikidata.md) &#8226; [__WikiPathways__](doc/wikipathways.md) 
+
+Miscellaneous utilities: [__UTIL__](doc/util.md) 
+
+## Usage Example
+
+```
+python3 -m bioclients.pubchem.Client -h
+```
+
+## Design pattern
+
+Generally each module includes command-line app `Client.py` which calls 
+functions in a corresponding `Utils.py`, providing all capabilities
+by import of the module. Command-line apps not API clients are generally 
+named `App.py`. Functions can write to an output file
+or return a Pandas dataframe (if output file unspecified).
+
+## Data structures and formats, XML, JSON, and TSV
+
+bioclients is designed to be simple and practical, and XML, JSON
+and TSV are likewise simple in many respects, yet a great deal
+of conceptual and technological progress is reflected. XML and JSON
+can represent arbitrarily complex data objects, comprised of nested lists,
+dictionaries, and trees of primary types. TSV represents tables of
+rows and columns, related by common keys, reflecting the development
+of SQL and relational databases. Transforming JSON to TSV, as these
+clients generally do, projects data objects to tables useful for many
+applications (e.g. machine learning).
+
+## Conda environment
+
+bioclients depends on numerous Python packages.  (See [conda/environment.yml](conda/environment.yml)).
+The following commands create and activate a Conda environment `bioclients`:
+
+```
+$ conda env create -f conda/environment.yml
+```
+If that fails, try:
+```
+$ conda create -n bioclients -c conda-forge pandas readline requests pyyaml tqdm psycopg2 numpy scipy scikit-learn matplotlib
+```
+then:
+```
+$ conda activate bioclients
+(bioclients) $ pip install bioclients
+```
+and install additional packages as needed via `pip`, e.g.:
+```
+(bioclients) $ pip install sqlalchemy
+(bioclients) $ pip install pyquery
+(bioclients) $ pip install mygene
+(bioclients) $ pip install click
+(bioclients) $ pip install PyMuPDF
+(bioclients) $ pip install py2neo
+```
+
+## Venv, etc.
+
+It may not be necessary or advantageous to configure an environment for all of bioclients functionality. Specific modules may be supported with `venv` environments with required dependencies. Module documentation should indicate needed package dependencies.

bioclients-0.2.33/README.md

@@ -0,0 +1,108 @@
+# `bioclients` <img align="right" src="doc/images/bioclients.png" height="120" alt="bioclients logo">
+
+Python package for access to online biomedical resources,
+usually via REST APIs. Modules generally include
+`Client.py` for command-line use and `Utils.py` for
+integration into other code. With the advent of HTTP web services,
+first SOAP/XML and then mostly REST/JSON, many online APIs
+require very similar methods for data search, requests
+and transforms into usable formats, often TSV.
+
+## Availability and installation
+
+### Installing from PyPI
+
+Releases at <https://pypi.org/project/bioclients/>.
+
+```
+pip3 install bioclients
+```
+However, current development snapshot may included additional functionality.
+
+### Installing from source
+
+Source at <https://github.com/jeremyjyang/bioclients>
+
+___(First download or clone.)___
+
+
+Install `build` package.
+
+```
+python3 -m pip install --upgrade build
+```
+
+Install using `build`.  This supercedes the deprecated `setup.py install` and `easy_install` methods.
+
+```
+cd bioclients
+python3 -m build
+```
+
+## Dependencies
+
+* Python 3.10+
+* Python packages: `pandas`, `requests`, `yaml`, `psycopg2`, `tqdm`, etc. (See [conda/environment.yml](conda/environment.yml)).
+
+## Modules
+
+ [__Allen__](doc/allen.md) &#8226; [__AMP-T2D__](doc/amp__t2d.md) &#8226; [__Badapple__](doc/badapple.md) &#8226; [__BindingDb__](doc/bindingdb.md) &#8226; [__BioGrid__](doc/biogrid.md) &#8226; [__BiomarkerKB__](doc/biomarkerkb.md) &#8226; [__Bioregistry__](doc/bioregistry.md) &#8226; [__BRENDA__](doc/brenda.md) &#8226; [__CAS__](doc/cas.md) &#8226; [__CDC__](doc/cdc.md) &#8226; [__CFDE__](doc/cfde.md) &#8226; [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) &#8226; [__ChEBI__](doc/chebi.md) &#8226; [__ChEMBL__](doc/chembl.md) &#8226; [__ChemIdPlus__](doc/chemidplus.md) &#8226; [__ClinicalTrials.gov__](doc/clinicaltrials.md) &#8226; [__Disease Ontology__](doc/diseaseontology.md) &#8226; [__DisGeNet__](doc/disgenet.md) &#8226; [__DNorm__](doc/dnorm.md) &#8226; [__DrugCentral__](doc/drugcentral.md) &#8226; [__EMBL-EBI__](doc/emblebi.md) &#8226; [__EnsEMBL__](doc/ensembl.md) &#8226; [__Entrez__](doc/entrez.md) &#8226; [__FDA__](doc/fda.md) &#8226; [__Gene Ontology__](doc/geneontology.md) &#8226; [__GTEx__](doc/gtex.md) &#8226; [__GWAS Catalog__](doc/gwascatalog.md) &#8226; [__HUGO__](doc/hugo.md) &#8226; [__HumanBase__](doc/humanbase.md) &#8226; [__iCite__](doc/icite.md) &#8226; [__IDG__](doc/idg.md) &#8226; [__JensenLab__](doc/jensenlab.md) &#8226; [__LINCS__](doc/lincs.md) &#8226; [__MaayanLab__](doc/maayanlab.md) &#8226; [__Medline__](doc/medline.md) &#8226; [__MeSH__](doc/mesh.md) &#8226; [__MONARCH__](doc/monarch.md) &#8226; [__MyGene__](doc/mygene.md) &#8226; [__NCBO__](doc/ncbo.md) &#8226; [__NCATS__](doc/ncats.md) &#8226; [__OMIM__](doc/omim.md) &#8226; [__OncoTree__](doc/oncotree.md) &#8226; [__Open Targets__](doc/opentargets.md) &#8226; [__Panther__](doc/panther.md) &#8226; [__PDB__](doc/pdb.md) &#8226; [__PubChem__](doc/pubchem.md) &#8226; [__PubMed__](doc/pubmed.md) &#8226; [__PubTator__](doc/pubtator.md) &#8226; [__Reactome__](doc/reactome.md) &#8226; [__RXNorm__](doc/rxnorm.md) &#8226; [__STRINGDB__](doc/stringdb.md) &#8226; [__TCGA__](doc/tcga.md) &#8226; [__TINX__](doc/tinx.md) &#8226; [__UBKG__](doc/ubkg.md) &#8226; [__UMLS__](doc/umls.md) &#8226; [__UniProt__](doc/uniprot.md) &#8226; [__Wikidata__](doc/wikidata.md) &#8226; [__WikiPathways__](doc/wikipathways.md) 
+
+Miscellaneous utilities: [__UTIL__](doc/util.md) 
+
+## Usage Example
+
+```
+python3 -m bioclients.pubchem.Client -h
+```
+
+## Design pattern
+
+Generally each module includes command-line app `Client.py` which calls 
+functions in a corresponding `Utils.py`, providing all capabilities
+by import of the module. Command-line apps not API clients are generally 
+named `App.py`. Functions can write to an output file
+or return a Pandas dataframe (if output file unspecified).
+
+## Data structures and formats, XML, JSON, and TSV
+
+bioclients is designed to be simple and practical, and XML, JSON
+and TSV are likewise simple in many respects, yet a great deal
+of conceptual and technological progress is reflected. XML and JSON
+can represent arbitrarily complex data objects, comprised of nested lists,
+dictionaries, and trees of primary types. TSV represents tables of
+rows and columns, related by common keys, reflecting the development
+of SQL and relational databases. Transforming JSON to TSV, as these
+clients generally do, projects data objects to tables useful for many
+applications (e.g. machine learning).
+
+## Conda environment
+
+bioclients depends on numerous Python packages.  (See [conda/environment.yml](conda/environment.yml)).
+The following commands create and activate a Conda environment `bioclients`:
+
+```
+$ conda env create -f conda/environment.yml
+```
+If that fails, try:
+```
+$ conda create -n bioclients -c conda-forge pandas readline requests pyyaml tqdm psycopg2 numpy scipy scikit-learn matplotlib
+```
+then:
+```
+$ conda activate bioclients
+(bioclients) $ pip install bioclients
+```
+and install additional packages as needed via `pip`, e.g.:
+```
+(bioclients) $ pip install sqlalchemy
+(bioclients) $ pip install pyquery
+(bioclients) $ pip install mygene
+(bioclients) $ pip install click
+(bioclients) $ pip install PyMuPDF
+(bioclients) $ pip install py2neo
+```
+
+## Venv, etc.
+
+It may not be necessary or advantageous to configure an environment for all of bioclients functionality. Specific modules may be supported with `venv` environments with required dependencies. Module documentation should indicate needed package dependencies.

bioclients-0.2.33/bioclients/__init__.py

@@ -0,0 +1 @@
+"""Python package for access to online biomedical resources, usually via REST APIs."""

bioclients-0.2.33/bioclients/allen/__init__.py

@@ -0,0 +1,3 @@
+"""Client tools for Allen Institute web services."""
+
+__all__ = [ "brain" ]

bioclients-0.2.33/bioclients/allen/brain/Client.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+#############################################################################
+### See: http://www.brain-map.org/api/index.html
+### http://help.brain-map.org/display/api/RESTful+Model+Access+%28RMA%29
+### 
+###  http://api.brain-map.org/api/v2/data/[Model]/[Model.id].[json|xml|csv]
+###
+###  http://api.brain-map.org/api/v2/data/Organism/1.xml
+###  http://api.brain-map.org/api/v2/data/Gene/15.xml
+###  http://api.brain-map.org/api/v2/data/Chromosome/12.json
+###  http://api.brain-map.org/api/v2/data/Structure/4005.xml
+###
+### http://api.brain-map.org/api/v2/data/Organism/query.json
+### http://api.brain-map.org/api/v2/data/Gene/describe.json
+### http://api.brain-map.org/api/v2/data/enumerate.json
+###
+###  http://api.brain-map.org/api/v2/data/Gene/
+###  http://api.brain-map.org/api/v2/data/Gene/18376.json
+### 
+###  &num_rows=[#]&start_row=[#]&order=[...]
+#############################################################################
+import sys,os,re,argparse,time,json,logging
+
+from ... import allen
+#
+##############################################################################
+if __name__=='__main__':
+  API_HOST='api.brain-map.org'
+  API_BASE_PATH='/api/v2'
+  PROG=os.path.basename(sys.argv[0])
+  ftype='SYMBOL';
+  ops = ["show_info", "list_probes"]
+  parser = argparse.ArgumentParser( description='AllenBrainAtlas REST API client')
+  parser.add_argument("op", choices=ops, help='OPERATION (select one)')
+  parser.add_argument("--i", dest="ifile", help="input file")
+  parser.add_argument("--ids", help="input IDs")
+  parser.add_argument("--o", dest="ofile", help="output (TSV)")
+  parser.add_argument("--api_host", default=API_HOST)
+  parser.add_argument("--api_base_path", default=API_BASE_PATH)
+  parser.add_argument("-v", "--verbose", action="count", default=0)
+  args = parser.parse_args()
+
+  logging.basicConfig(format='%(levelname)s:%(message)s', level=(logging.DEBUG if args.verbose>1 else logging.INFO))
+
+  api_base_url='https://'+args.api_host+args.api_base_path
+
+  fout = open(args.ofile, "w") if args.ofile else sys.stdout
+
+  ids=[]
+  if args.ifile:
+    fin = open(args.ifile)
+    while True:
+      line = fin.readline()
+      if not line: break
+      ids.append(line.rstrip())
+    fin.close()
+  elif args.ids:
+    ids = re.split('[, ]+', args.ids.strip())
+  if len(ids)>0: logging.info('Input IDs: %d'%(len(ids)))
+
+  t0=time.time()
+
+  if args.op=="show_info":
+    allen.brain.Utils.ShowInfo(api_base_url, fout)
+
+  elif args.op=="list_probes":
+    allen.brain.Utils.ListProbes(api_base_url, ids, fout)
+
+  else:
+    parser.error('Invalid operation: {0}'.format(args.op))
+
+  logging.info('Elapsed time: %s'%(time.strftime('%Hh:%Mm:%Ss', time.gmtime(time.time()-t0))))

bioclients-0.2.33/bioclients/allen/brain/Utils.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+#############################################################################
+### See: http://www.brain-map.org/api/index.html
+### http://help.brain-map.org/display/api/RESTful+Model+Access+%28RMA%29
+### 
+###  http://api.brain-map.org/api/v2/data/[Model]/[Model.id].[json|xml|csv]
+###
+###  http://api.brain-map.org/api/v2/data/Organism/1.xml
+###  http://api.brain-map.org/api/v2/data/Gene/15.xml
+###  http://api.brain-map.org/api/v2/data/Chromosome/12.json
+###  http://api.brain-map.org/api/v2/data/Structure/4005.xml
+###
+### http://api.brain-map.org/api/v2/data/Organism/query.json
+### http://api.brain-map.org/api/v2/data/Gene/describe.json
+### http://api.brain-map.org/api/v2/data/enumerate.json
+###
+###  http://api.brain-map.org/api/v2/data/Gene/
+###  http://api.brain-map.org/api/v2/data/Gene/18376.json
+### 
+###  &num_rows=[#]&start_row=[#]&order=[...]
+#############################################################################
+import sys,os,re,time,logging
+import urllib.parse,json
+
+from ...util import rest
+#
+##############################################################################
+def ShowInfo(base_url, fout):
+  rval = rest.Utils.GetURL(base_url+'/data/enumerate.json', parse_json=True)
+  print(json.dumps(rval, sort_keys=True, indent=2))
+
+
+##############################################################################
+def ListProbes(base_url, qrys, fout):
+  n_probe=0;
+  num_rows=0; start_row=0; total_rows=0;
+  for qry in qrys:
+    while True:
+      logging.debug('start_row = %d, num_rows = %d, total_rows = %d'%(start_row, num_rows, total_rows))
+      url_this = (base_url+"/data/query.json?start_row=%d&criteria=model::Probe,rma::criteria,gene[acronym$eq'%s']"%(start_row+num_rows, qry))
+      try:
+        rval = rest.Utils.GetURL(url_this, parse_json=True)
+      except Exception as e:
+        logging.error(e)
+        continue
+      success = rval['success'] if 'success' in rval else False
+      if not success:
+        break
+      id_this = rval['id'] if 'id' in rval else None
+      total_rows = rval['total_rows'] if 'total_rows' in rval else None
+      num_rows = rval['num_rows'] if 'num_rows' in rval else None
+      start_row = rval['start_row'] if 'start_row' in rval else None
+      probes = rval['msg'] if 'msg' in rval else []
+      for probe in probes:
+        n_probe+=1
+        if n_probe==1:
+          tags = sorted(probe.keys()) ##1st probe defines fields
+          fout.write('%s\n'%('\t'.join(['query','id']+tags)))
+        vals = [qry, id_this]+[(probe[tag] if tag in probe else '') for tag in tags]
+        fout.write('%s\n'%('\t'.join(vals)))
+      if start_row+num_rows >= total_rows:
+        break
+  logging.info('probes: %d'%n_probe)
+
+##############################################################################

bioclients-0.2.33/bioclients/allen/brain/__init__.py

@@ -0,0 +1 @@
+from .Utils import *

bioclients-0.2.33/bioclients/amp/__init__.py

@@ -0,0 +1,5 @@
+"""Client tools for AMP project web services."""
+
+#from .Utils import *
+
+__all__ = [ "t2d" ]

bioclients-0.2.33/bioclients/amp/t2d/Client.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+"""
+utility app for the AMP T2D REST API.
+http://www.type2diabetesgenetics.org/
+http://www.kp4cd.org/apis/t2d
+http://52.54.103.84/kpn-kb-openapi/
+
+DEPICT software (Pers, TH, et al., 2015)
+"""
+###
+import sys,os,re,json,argparse,time,logging
+#
+from ... import amp
+#
+API_HOST='public.type2diabeteskb.org'
+API_BASE_PATH='/dccservices'
+#
+#############################################################################
+if __name__=='__main__':
+  ops = ["list_tissues", "list_phenotypes", "depict_genepathway"]
+  parser = argparse.ArgumentParser(description="AMP T2D REST client")
+  parser.add_argument("op",choices=ops,help='operation')
+  parser.add_argument("--i", dest="ifile", help="input IDs file")
+  parser.add_argument("--ids", help="input IDs, comma-separated")
+  parser.add_argument("--gene", help="query gene (e.g. SLC30A8)")
+  parser.add_argument("--phenotype", default="T2D")
+  parser.add_argument("--max_pval", type=float, default=.0005)
+  parser.add_argument("--api_host", default=API_HOST)
+  parser.add_argument("--api_base_path", default=API_BASE_PATH)
+  parser.add_argument("--skip", type=int, default=0)
+  parser.add_argument("--nmax", type=int, default=0)
+  parser.add_argument("--o", dest="ofile", help="output (TSV)")
+  parser.add_argument("-v", "--verbose", default=0, action="count")
+  args = parser.parse_args()
+
+  logging.basicConfig(format='%(levelname)s:%(message)s', level=(logging.DEBUG if args.verbose>1 else logging.INFO))
+
+  BASE_URL = 'http://'+args.api_host+args.api_base_path
+
+  fout = open(args.ofile, "w") if args.ofile else sys.stdout
+
+  if args.ifile:
+    fin = open(args.ifile)
+    ids=[]
+    while True:
+      line = fin.readline()
+      if not line: break
+      ids.append(line.strip())
+    logging.info('input IDs: %d'%(len(ids)))
+    fin.close()
+  elif args.ids:
+    ids = re.split('[, ]+', args.ids.strip())
+
+  t0=time.time()
+
+  if args.op == 'list_tissues':
+    amp.t2d.ListTissues(BASE_URL, fout)
+
+  elif args.op == 'list_phenotypes':
+    amp.t2d.ListPhenotypes(BASE_URL, fout)
+
+  elif args.op == 'depict_genepathway':
+    amp.t2d.DepictGenePathway(BASE_URL, args.gene, args.phenotype, args.max_pval, fout)
+
+  else:
+    parser.error('Invalid operation: %s'%args.op)
+
+  logging.info('elapsed time: %s'%(time.strftime('%Hh:%Mm:%Ss', time.gmtime(time.time()-t0))))
+

bioclients-0.2.33/bioclients/amp/t2d/Utils.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python3
+"""
+Utilities for the AMP T2D REST API.
+http://www.type2diabetesgenetics.org/
+http://www.kp4cd.org/apis/t2d
+http://52.54.103.84/kpn-kb-openapi/
+
+DEPICT software (Pers, TH, et al., 2015)
+"""
+###
+import sys,os,re,json,time,logging
+#
+from ...util import rest
+#
+#############################################################################
+def ListTissues(base_url, fout):
+  rval = rest.Utils.GetURL(base_url+'/graph/tissue/list/object', parse_json=True)
+  tissues = rval["data"] if "data" in rval else []
+  tags = None; n_out=0;
+  for tissue in tissues:
+    logging.debug(json.dumps(tissue, indent=2))
+    if not tags:
+      tags = tissue.keys()
+      fout.write('\t'.join(tags)+'\n')
+    vals = [str(tissue[tag]) if tag in tissue else '' for tag in tags]
+    fout.write('\t'.join(vals)+'\n')
+    n_out += 1
+  logging.info("n_out: %d"%(n_out))
+
+#############################################################################
+def ListPhenotypes(base_url, fout):
+  rval=rest.Utils.GetURL(base_url+'/graph/phenotype/list/object', parse_json=True)
+  phenotypes = rval["data"] if "data" in rval else []
+  tags = None; n_out=0;
+  for phenotype in phenotypes:
+    logging.debug(json.dumps(phenotype, indent=2))
+    if not tags:
+      tags = phenotype.keys()
+      fout.write('\t'.join(tags)+'\n')
+    vals = [str(phenotype[tag]) if tag in phenotype else '' for tag in tags]
+    fout.write('\t'.join(vals)+'\n')
+    n_out += 1
+  logging.info("n_out: %d"%(n_out))
+
+##############################################################################
+def DepictGenePathway(base_url, gene, phenotype, max_pval, fout):
+  url = base_url+('/testcalls/depict/genepathway/object?gene=%s&phenotype=%s&lt_value=%f'%(gene, phenotype, max_pval))
+  rval = rest.Utils.GetURL(url, parse_json=True)
+  pathways = rval["data"] if "data" in rval else []
+  tags = None; n_out=0;
+  for pathway in pathways:
+    logging.debug(json.dumps(pathway, indent=2))
+    if not tags:
+      tags = pathway.keys()
+      fout.write('\t'.join(tags)+'\n')
+    vals = [str(pathway[tag]) if tag in pathway else '' for tag in tags]
+    fout.write('\t'.join(vals)+'\n')
+    n_out += 1
+  logging.info("n_out: %d"%(n_out))
+
+##############################################################################

bioclients-0.2.33/bioclients/amp/t2d/__init__.py

@@ -0,0 +1 @@
+from .Utils import *