Merge pull request #4 from reactome/develop

Develop to master

Author: teslajoy

reactome2py/content.py

@@ -1887,4 +1887,4 @@ def search_suggest(query='platele'):
     if response.status_code == 200:
         return response.json()
     else:
-        print('Status code returned a value of %s' % response.status_code)
+        print('Status code returned a value of %s' % response.status_code)

reactome2py/utils.py

@@ -0,0 +1,106 @@
+"""
+utility functions for Reactome data-fetch, mappings, and overlay networks
+"""
+from requests.exceptions import ConnectionError
+import requests
+import io
+import tarfile
+import zipfile
+
+
+def ehld_stids():
+    """
+    retrieves a list of high-level hierarchy pathway with Enhanced High Level Diagrams (EHLD)
+    https://reactome.org/icon-info/ehld-specs-guideline
+    :return: list of pathway stIds
+    """
+
+    url = "https://reactome.org/download/current/ehld/svgsummary.txt"
+
+    try:
+        response = requests.get(url=url)
+    except ConnectionError as e:
+        print(e)
+
+    if response.status_code == 200:
+        content_list = response.text.splitlines()
+        st_ids = [stId for stId in content_list if 'R-' in stId]
+        return st_ids
+    else:
+        print('Status code returned a value of %s' % response.status_code)
+
+
+def sbgn_stids():
+    """
+    retieves a list of lower-level (with hierarchy) pathways that have SBGNs
+    https://reactome.org/about/news/110-sbgn-files-revamp
+    :return: list of pathway stIds
+    """
+
+    url = "https://reactome.org/download/current/homo_sapiens.sbgn.tar.gz"
+
+    try:
+        response = requests.get(url=url)
+    except ConnectionError as e:
+        print(e)
+
+    if response.status_code == 200:
+        tar_file = tarfile.open(fileobj=io.BytesIO(response.content))
+        file_names = tar_file.getnames()
+        ehlds = ehld_stids()
+        sbgns = [f.replace('.sbgn', '') for f in file_names]
+        sbgn_only = list(set(sbgns) - set(ehlds))
+        return sbgn_only
+    else:
+        print('Status code returned a value of %s' % response.status_code)
+
+
+def _yield_zip(response):
+    """
+    read zipfile in memory
+    https://docs.python.org/3/library/zipfile.html
+    :param response:
+    :return: content of zip file
+    """
+
+    with zipfile.ZipFile(io.BytesIO(response.content)) as the_zip:
+        for zip_info in the_zip.infolist():
+            with the_zip.open(zip_info) as the_file:
+                yield the_file.readlines()
+
+
+def _read_ziplines(response):
+    """
+    helper function to clean zipline content parsing
+    :param response:
+    :return: list
+    """
+
+    return [c.split('\t') for c in [c.decode('utf8') for c in list(_yield_zip(response))[0]]]
+
+
+def gene_mappings():
+    """
+    Maps reactome pathway stId and name to it's associated gene list (HGNC)
+    :return: dictionary of reactome pathways and HGNC gene mappings to the pathway.
+    """
+
+    url = "https://reactome.org/download/current/ReactomePathways.gmt.zip"
+
+    try:
+        response = requests.get(url=url)
+    except ConnectionError as e:
+        print(e)
+
+    if response.status_code == 200:
+        gm = _read_ziplines(response)
+        relations = []
+
+        for i, e in enumerate(gm):
+            gm[i] = [s.strip() for s in gm[i]]
+            d = dict(name=gm[i][0], stId=gm[i][1], genes=gm[i][2:len(gm[i])])
+            relations.append(d)
+
+        return relations
+    else:
+        print('Status code returned a value of %s' % response.status_code)

setup.py

@@ -1,6 +1,6 @@
 from setuptools import setup, find_packages
 
-__version__ = '0.0.1'
+__version__ = '0.0.2'
 
 setup(
     name='reactome2py',
@@ -15,7 +15,7 @@
         'console_scripts': ['reactome2py = reactome2py.__main__:main']
     },
     install_requires=[
-        'requests'
+        'requests',
     ],
     extras_require={
         'pandas': ["pandas==0.24.2"],

tests/unit/test_utils.py

@@ -0,0 +1,13 @@
+from reactome2py import utils
+
+
+def test_ehld_stids():
+    assert isinstance(utils.ehld_stids(), list)
+
+
+def test_sbgn_stids():
+    assert isinstance(utils.sbgn_stids(), list)
+
+
+def test_gene_mappings():
+    assert isinstance(utils.gene_mappings()[0], dict)