addition of intact complex database

kinetic_datanator/data_source/intact.py

@@ -7,6 +7,9 @@
 from six.moves.urllib.request import urlretrieve
 import zipfile
 from six import BytesIO
+from ftplib import FTP
+import os
+
 
 Base = sqlalchemy.ext.declarative.declarative_base()
 
@@ -39,16 +42,81 @@ class ProteinInteractions(Base):
     stoich_b = Column(String(255))
     interaction_type = Column(String(255))
 
+class ProteinComplex(Base):
+    """ Represents protein complexes from the IntAct Database
+
+    Attributes:
+        identifier (:obj:`str`):
+        name (:obj:`str`):
+        ncbi (:obj:`str`):
+        subunits (:obj:`str`):
+        evidence (:obj:`str`):
+        go_annot (:obj:`str`):
+        desc (:obj:`str`):
+        source (:obj:`str`):
+    """
+    __tablename__ = 'Protein_Complex'
+
+    identifier = Column(String(255), primary_key = True)
+    name = Column(String(255))
+    ncbi = Column(String(255))
+    subunits = Column(String(255))
+    evidence = Column(String(255))
+    go_annot = Column(String(255))
+    desc = Column(String(255))
+    source = Column(String(255))
 
 class IntAct(data_source.HttpDataSource):
     """ A local SQLite copy of the IntAct Database"""
     base_model = Base
 
-    ENDPOINT_DOMAINS = {'intact' : 'ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip'}
+    ENDPOINT_DOMAINS = {'intact' : 'ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip',
+                        'complex' : 'ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/'}
+
 
     def load_content(self):
 
         #Downloads Content from FTP Server
+        self.add_complex()
+        self.add_interactions()
+
+    def add_complex(self):
+        if not os.path.exists(self.cache_dirname+'/intact_complex'):
+            os.makedirs(self.cache_dirname+'/intact_complex')
+
+        ftp = FTP('ftp.ebi.ac.uk')
+        ftp.login()
+        ftp.cwd('/pub/databases/intact/complex/current/complextab/')
+        filenames = ftp.nlst()
+        if not os.path.exists(self.cache_dirname+'/intact_complex/'+filenames[0]):
+            for filename in filenames:
+                local_filename = self.cache_dirname+'/intact_complex/'+filename
+                file = open(local_filename, 'wb')
+                ftp.retrbinary('RETR '+filename, file.write)
+                file.close()
+        ftp.quit()
+
+        columns = ['#Complex ac', 'Recommended name', 'Taxonomy identifier',
+        'Identifiers (and stoichiometry) of molecules in complex', 'Experimental evidence' ,
+        'Go Annotations', 'Description', 'Source']
+
+        new_columns = ['identifier', 'name', 'ncbi', 'subunits', 'evidence', 'go_annot', 'desc', 'source']
+
+        files = os.listdir(self.cache_dirname+'/intact_complex')
+        for tsv in files:
+            if 'README' in tsv:
+                continue
+            else:
+                dt = pd.read_csv(self.cache_dirname+'/intact_complex/'+tsv, delimiter = '\t', encoding='utf-8')
+                pand = dt.loc[:, columns]
+                pand.columns = new_columns
+                pand = pand.set_index('identifier')
+                pand.to_sql(name = 'Protein_Complex', con=self.engine, if_exists = 'append')
+                self.session.commit()
+
+
+    def add_interactions(self):
+
         if not self.cache_dirname + '/intact.txt':
             path = urlretrieve(self.ENDPOINT_DOMAINS['intact'])
             zipped = zipfile.ZipFile(BytesIO(path[0]))
@@ -70,18 +138,18 @@ def load_content(self):
         pand.to_sql(name = 'Protein_Interactions', con=self.engine, if_exists = 'replace', chunksize = 1000)
         self.session.commit()
 
-        # column_list = ["#ID(s) interactor A") , "ID(s) interactor B"), "Alt. ID(s) interactor A"),\
-        #     "Alt. ID(s) interactor B"), "Alias(es) interactor A"), "Alias(es) interactor B"),\
-        #     "Interaction detection method(s)"), "Publication 1st author(s)"), "Publication Identifier(s)"),\
-        #     "Taxid interactor A"), "Taxid interactor B"), "Interaction type(s)"), "Source database(s)"),\
-        #     "Interaction identifier(s)"), "Confidence value(s)"), "Expansion method(s)"), \
-        #     "Biological role(s) interactor A"), "Biological role(s) interactor B"), \
-        #     "Experimental role(s) interactor A"), "Experimental role(s) interactor B"), \
-        #     "Type(s) interactor A"), "Type(s) interactor B"), "Xref(s) interactor A"),\
-        #     "Xref(s) interactor B"), "Interaction Xref(s)"), "Annotation(s) interactor A"),\
-        #     "Annotation(s) interactor B"), "Interaction annotation(s)"), "Host organism(s)"), \
-        #     "Interaction parameter(s)"), "Creation date"), "Update date"), \
-        #     "Checksum(s) interactor A"), "Checksum(s) interactor B"), "Interaction Checksum(s)"),\
-        #     "Negative"), "Feature(s) interactor A"), "Feature(s) interactor B"),\
-        #     "Stoichiometry(s) interactor A"), "Stoichiometry(s) interactor B"), "Identification method participant A"), \
-        #     "Identification method participant B")]
+    # column_list = ["#ID(s) interactor A") , "ID(s) interactor B"), "Alt. ID(s) interactor A"),\
+    #     "Alt. ID(s) interactor B"), "Alias(es) interactor A"), "Alias(es) interactor B"),\
+    #     "Interaction detection method(s)"), "Publication 1st author(s)"), "Publication Identifier(s)"),\
+    #     "Taxid interactor A"), "Taxid interactor B"), "Interaction type(s)"), "Source database(s)"),\
+    #     "Interaction identifier(s)"), "Confidence value(s)"), "Expansion method(s)"), \
+    #     "Biological role(s) interactor A"), "Biological role(s) interactor B"), \
+    #     "Experimental role(s) interactor A"), "Experimental role(s) interactor B"), \
+    #     "Type(s) interactor A"), "Type(s) interactor B"), "Xref(s) interactor A"),\
+    #     "Xref(s) interactor B"), "Interaction Xref(s)"), "Annotation(s) interactor A"),\
+    #     "Annotation(s) interactor B"), "Interaction annotation(s)"), "Host organism(s)"), \
+    #     "Interaction parameter(s)"), "Creation date"), "Update date"), \
+    #     "Checksum(s) interactor A"), "Checksum(s) interactor B"), "Interaction Checksum(s)"),\
+    #     "Negative"), "Feature(s) interactor A"), "Feature(s) interactor B"),\
+    #     "Stoichiometry(s) interactor A"), "Stoichiometry(s) interactor B"), "Identification method participant A"), \
+    #     "Identification method participant B")]

tests/data_source/test_intact.py

@@ -21,13 +21,19 @@ def setUpClass(self):
     def tearDownClass(self):
         shutil.rmtree(self.cache_dirname)
 
-    def test_loading(self):
 
+    def test_add_complex(self):
+        q = self.intact.session.query(intact.ProteinComplex).get('EBI-1256672')
+
+        self.assertEqual(q.name, 'INO80 chromatin remodeling complex')
+        self.assertEqual(q.ncbi, '559292')
+        self.assertEqual(q.evidence, 'intact:EBI-1212520')
+
+
+    def test_add_interactions(self):
         q = self.intact.session.query(intact.ProteinInteractions).filter_by(interactor_a = 'uniprotkb:P27986').count()
         self.assertEqual(q, 274)
 
         q = self.intact.session.query(intact.ProteinInteractions).filter_by(interactor_a = 'uniprotkb:Q61824').first()
         self.assertEqual(q.interactor_b, 'uniprotkb:Q60631')
         self.assertEqual(q.publications, 'pubmed:11127814|mint:MINT-5213342')
-
-    #TODO: Add more Tests