Deprecating Bio.InterPro since it doesn't work with the current EBI I…

…nterPro website and uses the deprecate sgmllib module
biopython · Jul 6, 2010 · 9971d2c · 9971d2c
1 parent dcb66ed
commit 9971d2c
Show file tree

Hide file tree

Showing 9 changed files with 11 additions and 793 deletions.
diff --git a/Bio/InterPro/__init__.py b/Bio/InterPro/__init__.py
@@ -18,6 +18,11 @@
 
 """
 
+import warnings
+warnings.warn("Bio.InterPro is deprecated, and will be removed in a future "
+              "release of Biopython. Please get in contact via the mailing "
+              "lists if this is a problem for you.", DeprecationWarning)
+
 from Bio import File
 import sgmllib
 from Bio.SeqFeature import Reference
@@ -257,7 +262,7 @@ def get_interpro_entry( id ):
 
 if __name__ == '__main__':
     import Bio.File
-    handle = open('IPR001064.htm')
+    handle = get_interpro_entry('IPR001064')
     undo_handle = Bio.File.UndoHandle( handle )
     interpro_parser = InterProParser()
     record = interpro_parser.parse( handle )

diff --git a/DEPRECATED b/DEPRECATED
@@ -16,6 +16,11 @@ support for Python 2.4. This can be delayed given feedback from our users
 (e.g. if this proves to be a problem in combination with other libraries).
 An explicit warning was added to setup.py for Biopython 1.55.
 
+Bio.InterPro
+============
+This module was a parser for the EBI InterPro webpages, but no longer works
+with their current website. Deprecated in Release 1.55.
+
 Bio.GenBank.LocationParser
 ==========================
 This module used to be used for parsing GenBank and EMBL feature locations.

diff --git a/Tests/InterPro/IPR001064.htm b/Tests/InterPro/IPR001064.htm
diff --git a/Tests/InterPro/IPR001171.htm b/Tests/InterPro/IPR001171.htm