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RST fixes for DEPRECATED file
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Note still have a warning present from rst-lint from Bio.sequtils
vs Bio.SeqUtils, which is legitimate:

$ rst-lint DEPRECATED
INFO DEPRECATED:591 Duplicate implicit target name: bio.sequtils.
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@peterjc
peterjc committed Mar 1, 2017
1 parent b2c6061 commit 4774782
Showing 1 changed file with 52 additions and 53 deletions.
105 changes: 52 additions & 53 deletions DEPRECATED.rst
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Expand Up @@ -113,6 +113,21 @@ Declared obsolete with a PendingDeprecationWarning in Release 1.61, formally
deprecated in Release 1.62, removed in Release 1.67. Please use the newer
Bio.motifs module instead.

Before this, ``CompareAceParser`` and ``CompareAceConsumer`` from
``Bio.Motif.Parsers.AlignAce`` were declared obsolete in Release 1.53,
deprecated in Release 1.55 final, and removed in Release 1.57.

``AlignAceConsumer``, ``AlignAceParser``, and ``AlignAceScanner`` were
declared obsolete in Release 1.53 and deprecated in Release 1.55 final;
their functionality is now available through a read() function in
``Bio.Motif.Parsers.AlignAce``.

``MEMEParser``, ``_MEMEScanner``, ``_MEMEConsumer``, ``_MASTConsumer``,
``MASTParser``, ``_MASTScanner``, and ``MASTRecord`` were declared obsolete in
Release 1.54 and deprecated in Release 1.55 final; their functionality is now
available through a ``read()`` function in ``Bio.Motif.Parsers.MEME`` and
``Bio.Motif.Parsers.MAST``, respectively.

AlignAceCommandline and CompareAceCommandline
=============================================
Deprecated in release 1.62, removed in Release 1.67. An up to date version of
Expand Down Expand Up @@ -160,6 +175,9 @@ This module was a parser for the EBI InterPro webpages, but no longer worked
with their current website. Deprecated in Release 1.55, and removed in
Release 1.58.

Earlier the function ``pairlist_to_dict`` was deprecated in Release 1.45, and
removed in Release 1.53.

Bio.GenBank.LocationParser
==========================
This module used to be used for parsing GenBank and EMBL feature locations.
Expand Down Expand Up @@ -292,7 +310,7 @@ Declared obsolete in Release 1.49, deprecated in Release 1.51, and removed
in Release 1.57. Please use the methods or functions in Bio.Seq instead.

Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
==========================================
======================================================================
Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
deprecated in Release 1.50, Bio.listfns was deprecated in Release 1.53.
The three C implementations were all removed in Release 1.53. Bio.mathfns
Expand Down Expand Up @@ -336,7 +354,7 @@ in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
Bio.AlignIO instead.

Note that ``Bio.Fasta`` could be used with a ``RecordParser`` which gave
``FastaRecord`` objects, for example:
``FastaRecord`` objects, for example::

# Old code which won't work any more
from Bio import Fasta
Expand All @@ -348,7 +366,7 @@ Note that ``Bio.Fasta`` could be used with a ``RecordParser`` which gave
handle.close()

Alternatively using the old ``SequenceParser`` would give ``SeqRecord``
objects like those from the new ``Bio.SeqIO`` code, for example:
objects like those from the new ``Bio.SeqIO`` code, for example::

# Old code which won't work any more
from Bio import Fasta
Expand All @@ -358,7 +376,7 @@ objects like those from the new ``Bio.SeqIO`` code, for example:
print str(seq_record.seq) # The sequence as a string
handle.close()

Either of those examples using ``Bio.SeqIO`` becomes just:
Either of those examples using ``Bio.SeqIO`` becomes just::

# Updated versions of above examples using Bio.SeqIO instead
from Bio import SeqIO
Expand Down Expand Up @@ -559,19 +577,20 @@ list(SimpleFastaParser(handle)) from Bio.SeqIO.FastaIO instead (but
ideally convert your code to using an iterator approach).

Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
=======
The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
been deprecated as of Release 1.31, and removed in Release 1.43.
Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
==================================================================
The functions ``forward_complement`` and ``antiparallel`` in ``Bio.GFF.easy``
have been deprecated as of Release 1.31, and removed in Release 1.43.
Use the functions ``complement`` and ``reverse_complement`` in ``Bio.Seq``
instead.

The whole of the old Bio.GFF module was deprecated in Release 1.53, and removed
in Release 1.57 (with the intention of reusing this name space for a GFF
parser).
The whole of the old ``Bio.GFF`` module was deprecated in Release 1.53, and
removed in Release 1.57 (with the intention of reusing this name space for a
GFF parser).

Bio.sequtils
============
Deprecated as of Release 1.30, removed in Release 1.42.
Use Bio.SeqUtils instead.
Deprecated as of Release 1.30, removed in Release 1.42. Use ``Bio.SeqUtils``
instead.

Bio.SVM
=======
Expand All @@ -593,11 +612,6 @@ Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
the function kcluster in Bio.Cluster which performs k-means or k-medians
clustering.

Bio.InterPro
============
The function pairlist_to_dict was deprecated in Release 1.45, and removed in
Release 1.53.

Bio.SCOP
========
The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
Expand All @@ -617,20 +631,6 @@ and 'back_transcribe' were deprecated in Release 1.49, and removed in Release
The whole of Bio.utils was declared obsolete in Release 1.55, deprecated in
Release 1.56, and removed in Release 1.57.

Bio.Motif
=========
CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
declared obsolete in Release 1.53, deprecated in Release 1.55 final, and removed
in Release 1.57.
AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
in Release 1.53 and deprecated in Release 1.55 final; their functionality is
now available through a read() function in Bio.Motif.Parsers.AlignAce.
MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
_MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and
deprecated in Release 1.55 final; their functionality is now available through
a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST,
respectively.

Bio.Compass
===========
The RecordParser and Iterator classes were declared obsolete in Release 1.54,
Expand All @@ -643,11 +643,25 @@ The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
in Release 1.54, deprecated in Release 1.55 and removed in Release 1.59.
Their functionality is now available through a read() function.

Bio.PopGen.Async
================
``Bio.PopGen.Async`` was deprecated in Release 1.68. It will be removed in
Release 1.70.

Bio.PopGen.FDist
================
The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
in Release 1.54, deprecated in Release 1.55, and removed in Release 1.58.
Their functionality is now available through a read() function.
``Bio.PopGen.FDist`` was deprecated in Release 1.68. It will be removed in
Release 1.70.

Prior to this, the ``RecordParser``, ``_Scanner``, and ``_RecordConsumer``
classes were declared obsolete in Release 1.54, deprecated in Release 1.55,
and removed in Release 1.58. Their functionality is now available through
a ``read()`` function.

Bio.PopGen.SimCoal
==================
``Bio.PopGen.SimCoal`` was deprecated in Release 1.68. It will be removed in
Release 1.70.

Bio.UniGene
===========
Expand Down Expand Up @@ -677,23 +691,8 @@ deprecated in Release 1.57 and removed in Release 1.69.

Bio.ParserSupport
=================
Bio.ParserSupport was declared obsolete in Release 1.59, and deprecated in
Release 1.63. The Martel specific EventGenerator was removed in Release 1.67.
``Bio.ParserSupport`` was declared obsolete in Release 1.59, and deprecated in
Release 1.63. The Martel specific ``EventGenerator`` was removed in Release 1.67.

Bio.ParserSupport.SGMLStrippingConsumer was deprecated in Release 1.59, and
``Bio.ParserSupport.SGMLStrippingConsumer`` was deprecated in Release 1.59, and
removed in Release 1.61.

Bio.PopGen.Async
================
Bio.PopGen.Async was deprecated in Release 1.68. It will be removed in
Release 1.70.

Bio.PopGen.FDist
================
Bio.PopGen.FDist was deprecated in Release 1.68. It will be removed in
Release 1.70.

Bio.PopGen.SimCoal
==================
Bio.PopGen.SimCoal was deprecated in Release 1.68. It will be removed in
Release 1.70.

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