Merge pull request prody#1596 from jamesmkrieger/pfam-legacy

Interpro Pfam transition

prody/database/__init__.py

@@ -10,8 +10,7 @@
   * :func:`.fetchPfamMSA` - download MSA files
   * :func:`.searchPfam` - search for domain families of a protein
 
-
-.. _Pfam: http://pfam.sanger.ac.uk/
+.. _Pfam: https://www.ebi.ac.uk/interpro/entry/pfam/
 
 UniProt
 ========
@@ -70,7 +69,14 @@
 
 .. _GOA: https://www.ebi.ac.uk/GOA/
 
+Interpro
+====
+
+The following functions can be used to search and retrieve Pfam_ data:
+
+  * :func:`.searchInterpro` - search for domain families of a protein
 
+.. _Pfam: https://www.ebi.ac.uk/interpro/
 """
 
 __all__ = []
@@ -98,3 +104,7 @@
 from . import quartataweb
 from .quartataweb import *
 __all__.extend(quartataweb.__all__)
+
+from . import interpro
+from .interpro import *
+__all__.extend(interpro.__all__)

prody/database/interpro.py

@@ -0,0 +1,102 @@
+# -*- coding: utf-8 -*-
+"""This module defines functions for interfacing Interpro database."""
+
+__author__ = 'James Krieger'
+
+import json
+from os.path import isfile
+from prody import LOGGER, PY3K
+
+__all__ = ['searchInterpro']
+
+prefix = 'https://www.ebi.ac.uk/interpro/wwwapi/entry/'
+
+def searchInterpro(query, **kwargs):
+    """Returns Interpro search results in a list of dictionaries.  
+    
+    Matching family accessions as keys will map to various properties,
+    including start and end residue positions.
+
+    :arg query: UniProt ID or PDB identifier with or without a
+        chain identifier, e.g. ``'1mkp'`` or ``'1mkpA'``.  
+        UniProt ID of the specified chain, or the first
+        protein chain will be used for searching the Pfam database
+    :type query: str
+
+    :arg timeout: timeout for blocking connection attempt in seconds, default
+        is 60
+    :type timeout: int
+    """
+    import requests
+
+    LOGGER.timeit('_interpro')
+    timeout = int(kwargs.get('timeout', 60))
+
+    if len(query) == 4:
+        url = prefix + "all/structure/pdb/" + query
+
+    elif len(query) == 5:
+        accession = None
+
+        from prody import parsePDBHeader
+        try:
+            polymers = parsePDBHeader(query[:4], 'polymers')
+        except Exception as err:
+            raise ValueError('failed to parse header for {0} ({1})'
+                             .format(query[:4], str(err)))
+
+        chid = query[4:].upper()
+
+        for poly in polymers:
+            if chid and poly.chid != chid:
+                continue
+            for dbref in poly.dbrefs:
+                if dbref.database != 'UniProt':
+                    continue
+                accession = dbref.accession
+                LOGGER.info('UniProt accession {0} for {1} chain '
+                            '{2} will be used.'
+                            .format(accession, query[:4], poly.chid))
+                break
+            if accession is not None:
+                break
+
+        if accession is None:
+            raise ValueError('A UniProt accession for PDB {0} could not be '
+                             'parsed.'.format(repr(query)))
+        else:
+            url = prefix + "all/protein/uniprot/" + accession
+
+    else:
+        url = prefix + "all/protein/uniprot/" + query
+
+    LOGGER.debug('Retrieving Interpro search results: ' + url)
+    result = None
+    sleep = 2
+    while LOGGER.timing('_interpro') < timeout:
+        try:
+            result = requests.get(url, verify=False).content
+        except Exception:
+            pass
+        else:
+            if result not in ['PEND','RUN']:
+                break
+
+        sleep = 20 if int(sleep * 1.5) >= 20 else int(sleep * 1.5)
+        LOGGER.sleep(int(sleep), '. Trying to reconnect...')
+
+    if not result:
+        raise IOError('Interpro search timed out or failed to parse results, '
+                      ' check URL: ' + url)
+    else:
+        LOGGER.report('Interpro search completed in %.2fs.', '_interpro')
+
+    if PY3K:
+        result = result.decode()
+
+    try:
+        result = json.loads(result)
+    except Exception as err:
+        raise ValueError('failed to parse results as json, check URL: ' + url)
+
+    return result["results"]