@@ -1,4 +1,7 @@ -"""This module contains code to access EZRetrieve (OBSOLETE). +"""This module contains code to access EZRetrieve (DEPRECATED). + +This module is now deprecated, and will be removed in a future release of +Biopython. This is a very simple interface to the EZRetrieve website described in: @@ -11,11 +14,15 @@ http://dx.doi.org/10.1093/nar/gnf120 Functions: retrieve_single Retrieve a single sequence from EZRetrieve. parse_single Parse the results from EZRetrieve into FASTA format. - -This module is now considered to be obsolete, and is likely to be deprecated -in a future release of Biopython, and later removed. """ +import warnings +warnings.warn("Bio.EZRetrieve is deprecated, and will be removed in a future"\ + " release of Biopython. If you want to continue to use this"\ + " code, please get in contact with the Biopython developers"\ + " via the mailing lists to avoid its permanent removal from"\ + " Biopython.", DeprecationWarning) + def retrieve_single(id, from_, to, retrieve_by=None, organism=None, parse_results=1): import urllib Bio/EZRetrieve.py @@ -7,9 +7,13 @@ Classes: + UndoHandle File object decorator with support for undo-like operations. + StringHandle Wraps a file object around a string. -SGMLHandle File object that automatically strips SGML tags from data. + +SGMLHandle File object that automatically strips SGML tags from data + (DEPRECATED). SGMLStripper Object that strips SGML. This is now considered OBSOLETE, and is likely to be deprecated in a future release of Biopython, @@ -107,10 +111,8 @@ class UndoHandle: # readlines method. StringHandle = StringIO.StringIO - - class SGMLHandle: - """A Python handle that automatically strips SGML tags from data (OBSOLETE). + """A Python handle that automatically strips SGML tags from data (DEPRECATED). This module is now considered to be obsolete, and is likely to be deprecated in a future release of Biopython, and later removed. @@ -121,6 +123,12 @@ class SGMLHandle: handle is a file handle to SGML-formatted data. """ + import warnings + warnings.warn("Bio.File.SGMLHandle is deprecated, and will be removed"\ + " in a future release of Biopython. If you want to"\ + " continue to use this code, please get in contact via"\ + " the mailing lists to avoid its permanent removal from"\ + " Biopython.", DeprecationWarning) self._handle = handle self._stripper = SGMLStripper() Bio/File.py @@ -3,7 +3,10 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -"""Code for more fancy file handles (OBSOLETE). +"""Code for more fancy file handles (DEPRECATED). + +This module is now deprecated, and will be removed in a future release of +Biopython. Classes: Filtered is a decorator for File that allows the user to filter the output @@ -20,11 +23,14 @@ filtered_reasder.read() All filters in the chain must provide the same interface with a line of text as the single input parameter and altered text as the return value. - -This module is now considered to be obsolete, and is likely to be deprecated -in a future release of Biopython, and later removed. """ +import warnings +warnings.warn("Bio.FilteredReader is deprecated, and will be removed in a"\ + " future release of Biopython. If you want to continue to use"\ + " this code, please get in contact with the developers"\ + " via the mailing lists to avoid its permanent removal from"\ + " Biopython.", DeprecationWarning) def dump_saved( name, text, j ): """Used for debugging.""" Bio/FilteredReader.py @@ -3,7 +3,10 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -"""Code for dealing with lists of URLs (OBSOLETE). +"""Code for dealing with lists of URLs (DEPRECATED). + +This module is now deprecated, and will be removed in a future release of +Biopython. NetCatch enables the user to scan a list of labelled urls and select a subset to read into a file. @@ -13,10 +16,14 @@ get_urls_by_label get_urls_by_index get_urls_by_range select_output_file - -This module is now considered to be obsolete, and is likely to be deprecated -in a future release of Biopython, and later removed. """ + +import warnings +warnings.warn("Bio.NetCatch is deprecated, and will be removed in a future"\ + " release of Biopython. If you want to continue to use this"\ + " code, please get in contact with the Biopython developers"\ + " via the mailing lists to avoid its permanent removal from"\ + " Biopython.", DeprecationWarning) import os import urllib import sgmllib Bio/NetCatch.py @@ -49,7 +49,7 @@ Bio.ExPASy.Enzyme, respectively. Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader ===================================================================== -Declared obsolete in Release 1.50, will be deprecated in a subsequent release. +Declared obsolete in Release 1.50, deprecated in Release 1.52. Bio.Graphics.GenomeDiagram and colour/color, centre/center ========================================================== DEPRECATED 2b32b9365a3f6553e733f6e652ca0cc961895d1a peterc peterc http://github.com/etal/biopython/commit/bc953faeb82f9906110e3480af4bb48cae0807f3 bc953faeb82f9906110e3480af4bb48cae0807f3 2009-09-10T03:25:16-07:00 2009-09-10T03:25:16-07:00 Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle and Bio.FilteredReader (declared obsolete in 1.50) 120e998c82240e2311000218aa3e4ca6f8f2403e peterc peterc