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Removing the deprecated code

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1 parent 0433a74 commit 8dc36665ef103ae92eab2b404ec8736ea81fa7bf Michiel de Hoon committed Aug 28, 2010
Showing with 2 additions and 25 deletions.
  1. +0 −15 Bio/Emboss/Applications.py
  2. +0 −9 Bio/Entrez/__init__.py
  3. +2 −1 DEPRECATED
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@@ -464,21 +464,6 @@ def __init__(self, cmd="primersearch", **kwargs):
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
- def set_parameter(self, name, value=None):
- #Due to a historical inconsistency, the PrimerSearchCommandline
- #wrapper used -out and out, rather than -output and output like all
- #the other EMBOSS wrappers. I want to implement this paramter via
- #the common _EmbossCommandLine base class, hence this hack for
- #backwards compatibility:
- if name in ["out", "-out"]:
- import warnings
- warnings.warn('Aliases "-out" and "out" are deprecated, please use '
- 'either "-outfile" or "outfile" with set_parameter '
- 'instead, or use the outfile property.',
- DeprecationWarning)
- name = "outfile"
- _EmbossCommandLine.set_parameter(self, name, value)
-
class EProtDistCommandline(_EmbossCommandLine):
"""Commandline object for the eprotdist program from EMBOSS (DEPRECATED).
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@@ -93,15 +93,6 @@ def efetch(db, **keywds):
handle = Entrez.efetch(db="nucleotide", id="57240072", rettype="gb")
print handle.read()
"""
- for key in keywds:
- if key.lower()=="rettype" and keywds[key].lower()=="genbank":
- warnings.warn('As of Easter 2009, Entrez EFetch no longer '
- 'supports the unofficial return type "genbank", '
- 'use "gb" or "gp" instead.', DeprecationWarning)
- if db.lower()=="protein":
- keywds[key] = "gp" #GenPept
- else:
- keywds[key] = "gb" #GenBank
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
variables = {'db' : db}
variables.update(keywds)
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@@ -86,7 +86,8 @@ Bio.Entrez.efetch and rettype="genbank"
As of Easter 2009, the NCBI have stopped supporting the unofficial return type
of "genbank" in EFetch. Instead we should be using "gb" (GenBank) or "gp"
(GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
-automatically, but issues a deprecation warning.
+automatically, but issues a deprecation warning. The code to check and correct
+for "genbank" was removed in Biopython 1.55 final.
Bio.Entrez.query function
=========================

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