diff uniprot.py @ 1:cd2a41c65447 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489

--- a/uniprot.py	Fri Oct 09 16:42:22 2015 -0400
+++ b/uniprot.py	Fri Oct 14 17:59:02 2016 -0400
@@ -8,12 +8,14 @@
     map
     retrieve
 """
+import argparse
+import sys
 
 import requests
-import sys, argparse
 
 url = 'http://www.uniprot.org/'
 
+
 def _retrieve(query, format='txt'):
     """_retrieve is not meant for use with the python interface, use `retrieve`
     instead"""
@@ -22,25 +24,12 @@
     query = list(set(query.split('\n')))
     queries = [query[i:i+100] for i in range(0, len(query), 100)]
 
-    data = {'format':format}
+    data = {'format': format}
 
-    responses = [requests.post(url + tool, data=data, files={'file':' '.join(query)}) for query in queries]
-    page = ''.join([response.text for response in responses])
+    responses = [requests.post(url + tool, data=data, files={'file': ' '.join(_)}) for _ in queries]
+    page = ''.join(response.text for response in responses)
     return page
 
-def retrieve(ids, format='txt'):
-    """ request entries by uniprot acc using batch retrieval
-
-    Args:
-        query: list of ids to retrieve
-        format: txt by default
-
-    Help:
-        possible formats:
-        txt, xml, rdf, fasta, gff"""
-    if type(ids) is not list:
-        ids = [ids]
-    return _retrieve(' '.join(ids), format)
 
 def _map(query, f, t, format='tab'):
     """ _map is not meant for use with the python interface, use `map` instead
@@ -48,44 +37,17 @@
     tool = 'mapping/'
 
     data = {
-            'from':f,
-            'to':t,
-            'format':format,
+            'from': f,
+            'to': t,
+            'format': format,
             'query': query
             }
     response = requests.post(url + tool, data=data)
     page = response.text
     return page
 
-def map(ids, f, t, format='tab'):
-    """ map a list of ids from one format onto another using uniprots mapping api
-    
-    Args:
-        query: id or list of ids to be mapped
-        f: from ACC | P_ENTREZGENEID | ...
-        t: to ...
-        format: tab by default
-
-    Help:
-        for a list of all possible mappings visit
-        'http://www.uniprot.org/faq/28'
-    """
-    if type(ids) is not list:
-        ids = [ids]
-    page = _map(' '.join(ids), f, t, format)
-    result = dict()
-    for row in page.splitlines()[1:]:
-        key, value = row.split('\t')
-        if key in result:
-            result[key].add(value)
-        else:
-            result[key] = set([value])
-    return result
 
 if __name__ == '__main__':
-    import argparse
-    import sys
-
     parser = argparse.ArgumentParser(description='retrieve uniprot mapping')
     subparsers = parser.add_subparsers(dest='tool')
 
@@ -93,16 +55,16 @@
     mapping.add_argument('f', help='from')
     mapping.add_argument('t', help='to')
     mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'),
-            default=sys.stdin, help='input file (default: stdin)')
+                         default=sys.stdin, help='input file (default: stdin)')
     mapping.add_argument('out', nargs='?', type=argparse.FileType('w'),
-            default=sys.stdout, help='output file (default: stdout)')
+                         default=sys.stdout, help='output file (default: stdout)')
     mapping.add_argument('--format', default='tab', help='output format')
 
     retrieve = subparsers.add_parser('retrieve')
-    retrieve.add_argument('inp', metavar = 'in', nargs='?', type=argparse.FileType('r'),
-            default=sys.stdin, help='input file (default: stdin)')
+    retrieve.add_argument('inp', metavar='in', nargs='?', type=argparse.FileType('r'),
+                          default=sys.stdin, help='input file (default: stdin)')
     retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'),
-            default=sys.stdout, help='output file (default: stdout)')
+                          default=sys.stdout, help='output file (default: stdout)')
     retrieve.add_argument('-f', '--format', help='specify output format', default='txt')
 
     args = parser.parse_args()
@@ -113,5 +75,3 @@
 
     elif args.tool == 'retrieve':
         args.out.write(_retrieve(query, format=args.format))
-
-