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Update DEPRECATED file after Bio.EUtils removal etc

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commit 2619bcbe53c1d4c10f35d3aac50ec0140dd7ee08 1 parent 5c2119c
@peterjc peterjc authored
Showing with 14 additions and 7 deletions.
  1. +14 −7 DEPRECATED
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21 DEPRECATED
@@ -27,8 +27,12 @@ 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). Bio.Entrez.efetch will correct this automatically, but issues a
-deprecation warning.
+(GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
+automatically, but issues a deprecation warning.
+
+Bio.Entrez.query function
+=========================
+Deprecated in Release 1.47, removed in 1.52.
Bio.SwissProt.SProt
===================
@@ -146,19 +150,22 @@ Please use Bio.Entrez instead.
Bio.EUtils
==========
-Deprecated in favor of Bio.Entrez in Release 1.48.
+Deprecated in favor of Bio.Entrez in Release 1.48, removed in Release 1.52.
-Bio.Sequencing
-==============
-A revised API was added and the old one deprecated in Biopython 1.48:
+Bio.Sequencing & Bio.Medline
+============================
+A revised API was added and the old one deprecated in Release 1.48,
+and removed in Biopython 1.52:
Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
+Bio.Medline.RecordParser --> Bio.Medline.read(handle)
+Bio.Medline.Iterator --> Bio.Medline.parse(handle)
Bio.Blast.NCBIWWW
=================
-The HTML BLAST parser was deprecated as of Release 1.48.
+The HTML BLAST parser was deprecated in Release 1.48, and removed in 1.52.
The deprecated functions blast and blasturl were removed in Release 1.44.
Bio.Saf
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