Removed spaces in empty lines in inputs module

src/pypath/inputs/__init__.py

@@ -18,7 +18,6 @@
 #  Website: http://pypath.omnipathdb.org/
 #
 
-
 import importlib
 
 
@@ -31,35 +30,35 @@ def get_method(module_name, method_name = None):
     name. E.g. for ``'uniprot.all_uniprots'`` it returns the ``all_uniprots``
     method from the ``pypath.inputs.uniprot`` module.
     """
-    
+
     if not method_name:
-        
+
         module_method = module_name.rsplit('.', maxsplit = 1)
         method_name = module_method[-1]
         module_name = module_method[-2] if len(module_method) > 1 else 'main'
-    
+
     module_name = module_name.rsplit('.', maxsplit = 1)[-1]
     module_name = 'pypath.inputs.%s' % module_name
-    
+
     try:
-        
+
         mod = importlib.import_module(module_name)
-        
+
     except:
-        
+
         session.get_log().msg(
             msg = 'Could not import module `%s`.' % module_name,
             label = 'inputs',
         )
-        
+
     try:
-        
+
         method = getattr(mod, method_name)
-        
+
         return method
-        
+
     except:
-        
+
         session.get_log().msg(
             msg = 'Could not find method `%s` in module `%s`.' % (
                 method_name,

src/pypath/inputs/deathdomain.py

@@ -83,11 +83,11 @@ def deathdomain_interactions_rescued():
     """
 
     url = urls.urls['death']['url_alive']
-    
+
     c = curl.Curl(url, silent = False, large = True)
-    
+
     _ = next(c.result)
-    
+
     return [
         [i.strip() for i in line.split('\t')]
         for line in c.result

src/pypath/inputs/depod.py

@@ -47,17 +47,17 @@ def depod_interactions(organism = 9606):
         l = l.split('\t')
         specA = int(l[9].split(':')[1].split('(')[0])
         specB = int(l[10].split(':')[1].split('(')[0])
-        
+
         if organism is None or (specA == organism and specB == organism):
-            
+
             pm = l[8].replace('pubmed:', '')
             sc = l[14].replace('curator score:', '')
             ty = l[11].split('(')[1].replace(')', '')
             l = [l[0], l[1]]
             interaction = ()
-            
+
             for ll in l:
-                
+
                 ll = ll.split('|')
                 uniprot = ''
                 for lll in ll:
@@ -66,38 +66,38 @@ def depod_interactions(organism = 9606):
                     if nm[0] == 'uniprotkb' and len(u) == 6:
                         uniprot = u
                 interaction += (uniprot, )
-            
+
             interaction += (pm, sc, ty)
             if len(interaction[0]) > 1 and len(interaction[1]) > 1:
                 i.append(interaction)
-        
+
         lnum += 1
 
     return i
 
 
 def depod_enzyme_substrate(organism = 9606):
-    
+
     result = []
-    
+
     reunip = re.compile(r'uniprotkb:([A-Z0-9]+)')
     reptm = re.compile(r'([A-Z][a-z]{2})-([0-9]+)')
     repmidsep = re.compile(r'[,|]\s?')
-    
+
     url = urls.urls['depod']['urls'][0]
     c = curl.Curl(url, silent = False, encoding = 'ascii')
     data = c.result
     data = [x.split('\t') for x in data.split('\n')]
     del data[0]
-    
+
     url_mitab = urls.urls['depod']['urls'][1]
     c_mitab = curl.Curl(url_mitab, silent = False, encoding = 'iso-8859-1')
     data_mitab = c_mitab.result
     data_mitab = [x.split('\t') for x in data_mitab.split('\n')]
     del data_mitab[0]
-    
+
     for i, l in enumerate(data):
-        
+
         if (
             len(l) > 6 and
             l[2] == 'protein substrate' and
@@ -106,10 +106,10 @@ def depod_enzyme_substrate(organism = 9606):
             ) == organism and
             l[4].strip() != 'N/A'
         ):
-            
+
             enzyme_uniprot = reunip.search(data_mitab[i][0]).groups()[0]
             substrate_uniprot = reunip.search(data_mitab[i][1]).groups()[0]
-            
+
             for enzyme_up, substrate_up in itertools.product(
                     mapping.map_name(
                         enzyme_uniprot,
@@ -122,16 +122,16 @@ def depod_enzyme_substrate(organism = 9606):
                         'uniprot'
                     ),
                 ):
-                
+
                 for resaa, resnum in reptm.findall(l[4]):
-                    
+
                     resnum = int(resnum)
                     resaa = (
                         common.aminoa_3_to_1_letter[resaa]
                             if resaa in common.aminoa_3_to_1_letter else
                         resaa
                     )
-                    
+
                     result.append({
                         'instance': None,
                         'kinase': enzyme_up,
@@ -143,5 +143,5 @@ def depod_enzyme_substrate(organism = 9606):
                         'end': None,
                         'typ': 'dephosphorylation',
                     })
-    
+
     return result

src/pypath/inputs/huri.py

@@ -93,23 +93,23 @@ def hi_iii():
         'form[request_file_format]': 'psi',
     }
     c = curl.Curl(url, silent = False, large = True, post = post_data)
-    
+
     for row in c.result:
-        
+
         if not row.strip():
-            
+
             continue
-        
+
         id_a, id_b, rest = row.split(' ', maxsplit = 2)
         id_a, isoform_a = id_a.split('-') if '-' in id_a else (id_a, 1)
         id_b, isoform_b = id_b.split('-') if '-' in id_b else (id_b, 1)
-        
+
         sc = rescore.search(rest)
         score = float(sc.groups()[0]) if sc else None
         screens = tuple(
             int(i) for i in rescreens.search(rest).groups()[0].split(',')
         )
-        
+
         yield HiiiiInteraction(
             id_a = id_a[10:],
             id_b = id_b[10:],
@@ -122,11 +122,11 @@ def hi_iii():
 
 def lit_bm_13_interactions():
     """
-    Downloads and processes Lit-BM-13 dataset, the 2013 version of the 
+    Downloads and processes Lit-BM-13 dataset, the 2013 version of the
     high confidence literature curated interactions from CCSB.
     Returns list of interactions.
     """
-    
+
     LitBm13Interaction = collections.namedtuple(
         'LitBm13Interaction',
         [
@@ -136,16 +136,16 @@ def lit_bm_13_interactions():
             'genesymbol_b',
         ]
     )
-    
+
     url = urls.urls['hid']['lit-bm-13']
     c = curl.Curl(url, silent = False, large = True)
-    
+
     _ = next(c.result)
-    
+
     for row in c.result:
-        
+
         row = row.strip().split('\t')
-        
+
         yield LitBm13Interaction(
             entrez_a = row[0],
             entrez_b = row[2],
@@ -156,11 +156,11 @@ def lit_bm_13_interactions():
 
 def lit_bm_17_interactions():
     """
-    Downloads and processes Lit-BM-13 dataset, the 2017 version of the 
+    Downloads and processes Lit-BM-13 dataset, the 2017 version of the
     high confidence literature curated interactions from CCSB.
     Returns list of interactions.
     """
-    
+
     LitBm17Interaction = collections.namedtuple(
         'LitBm17Interaction',
         [
@@ -170,25 +170,25 @@ def lit_bm_17_interactions():
             'score',
         ]
     )
-    
+
     url = urls.urls['hid']['lit-bm-17']
     c = curl.Curl(url, silent = False)
     data = c.result
-    
+
     c = curl.Curl(url, silent = False, large = True)
-    
+
     _ = next(c.result)
-    
+
     for row in c.result:
-        
+
         row = row.strip().split('\t')
-        
+
         id_a = row[0][10:]
         id_b = row[1][10:]
-        
+
         pubmed = row[8][7:]
         score = float(row[14][13:])
-        
+
         yield LitBm17Interaction(
             id_a = id_a,
             id_b = id_b,

src/pypath/inputs/intact.py

@@ -80,9 +80,9 @@ def get_id(field):
             uniprot, isoform = _try_isoform(
                 field.split(':')[1].replace('"', '')
             )
-            
+
             uniprot = uniprot.split('-')[0]
-            
+
             return uniprot, isoform
 
 

src/pypath/inputs/kea.py

@@ -19,7 +19,6 @@
 #  Website: http://pypath.omnipathdb.org/
 #
 
-
 import re
 import collections
 import itertools
@@ -40,8 +39,8 @@
 
 
 def kea_interactions():
-    
-    
+
+
     KeaRecord = collections.namedtuple(
         'KeaRecord',
         [
@@ -53,32 +52,32 @@ def kea_interactions():
             'resource',
         ]
     )
-    
+
     resub = re.compile(r'(\w+)_([A-Z])([0-9]+)')
-    
+
     url = urls.urls['kea']['kinase_substrate']
-    
+
     c = curl.Curl(url, silent = False, large = True)
-    
+
     result = []
-    
+
     for rec in c.result:
-        
+
         rec = rec.strip().split('\t')
-        
+
         site = resub.match(rec[1].strip())
-        
+
         if not site:
-            
+
             continue
-        
+
         target, resaa, resnum = site.groups()
-        
+
         e_uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
         s_uniprots = mapping.map_name(target, 'genesymbol', 'uniprot')
-        
+
         for enz, sub in itertools.product(e_uniprots, s_uniprots):
-            
+
             result.append(
                 KeaRecord(
                     enzyme = enz,
@@ -89,12 +88,12 @@ def kea_interactions():
                     resource = _resources[rec[3].strip()]
                 )
             )
-    
+
     return result
 
 
 def kea_enzyme_substrate():
-    
+
     return [
         {
             'start': None,