Manually improving markup and code style of multiple pages.

Author: MarkusPiotrowski

wiki/Degenerated_Codons.md

@@ -1,5 +1,5 @@
 ---
-title: Degenerated Codons
+title: Methods for Degenerated Codons
 permalink: wiki/Degenerated_Codons
 layout: wiki
 redirect_from:
@@ -19,15 +19,16 @@ Solution
 ``` python
 from Bio.Data.CodonTable import unambiguous_dna_by_id
 
-def altcodons( codon, table ):
-    """
-    list codons that code for the same aminoacid / are also stop
+
+def altcodons(codon, table):
+    """List codons that code for the same aminonacid / are also stop.
+
     @param codon
     @table code table id
     @return list of codons
-    """
 
-    tab = unambiguous_dna_by_id[ table ]
+    """
+    tab = unambiguous_dna_by_id[table]
 
     if codon in tab.stop_codons:
         return tab.stop_codons
@@ -37,42 +38,39 @@ def altcodons( codon, table ):
     except:
         return []
 
-    return [k for ( k, v ) in tab.forward_table.iteritems() if v == aa and k[0] == codon[0] and k[1] == codon[1]]
+    return [k for (k, v) in tab.forward_table.iteritems()
+            if v == aa and k[0] == codon[0] and k[1] == codon[1]]
+
+
+def degeneration(codon, table):
+    """Determine how many codons code for the same amino acid / are also stop
 
-def degeneration( codon, table ):
-    """
-    determine how many codons code for the same amino acid / are also stop
-    as codon
-    
     @param codon the codon
-    @param table code table id 
-    @param the number of codons also coding for the aminoacid codon codes for
+    @param table code table id
+    @param the number of codons also coding for the amino acid codon codes for
+
     """
+    return len(altcodons(codon, table))
 
-    return len( altcodons( codon, table ) )
 
-def isXdegenerated( x, codon, table ):
-    """
-    determine if codon is x-fold degenerated
+def is_x_degenerated(x, codon, table):
+    """Determine if codon is x-fold degenerated.
 
     @param codon the codon
-    @param table code table id  
+    @param table code table id
     @param true if x <= the degeneration of the codon
-    """
-
-    return ( x <= len( altcodons( codon, table ) ) )
 
-def degenerated_subseq( seq, x, table ):
-    """
-    get a subsequence consisting of the x-fold degenerated codons only
     """
+    return (x <= len(altcodons(codon, table)))
+
 
+def degenerated_subseq(seq, x, table):
+    """Get a subsequence consisting of the x-fold degenerated codons only."""
     data = ""
-    for i in range( 0, len( seq ), 3 ):
+    for i in range(0, len(seq), 3):
         codon = seq[i:i + 3].tostring()
-        if isXdegenerated( x, codon, table ):
+        if isXdegenerated(x, codon, table):
             data += codon
     return data
-```
 
-<category:Cookbook>
+```

wiki/Deprecation_policy.md

@@ -11,15 +11,15 @@ remove such code from Biopython, while avoiding any nasty surprises for
 users who may be relying on older code.
 
 We keep a plain text file in the Biopython source code to record these
-changes, available
-[here](http://biopython.open-bio.org/SRC/biopython/DEPRECATED) or on
-[github](http://github.com/biopython/biopython/blob/master/DEPRECATED).
+changes, available on 
+[GitHub](http://github.com/biopython/biopython/blob/master/DEPRECATED) or
+[here](http://biopython.open-bio.org/SRC/biopython/DEPRECATED).
 
 This is the current policy for deprecating and removing code from
 Biopython:
 
 -   First, ask on the biopython and biopython-dev [mailing
-    lists](mailing_lists "wikilink") whether a given piece of code has
+    lists](Mailing_lists "wikilink") whether a given piece of code has
     any users. Please keep in mind that not all users are following the
     biopython-dev mailing list.
 -   Consider declaring the module as "obsolete" for a release
@@ -35,13 +35,15 @@ Biopython:
         ideally with examples or a reference to the tutorial.
     -   Most importantly, add a DeprecationWarning to the code:
 
-`import warnings`  
-`warnings.warn("Bio.SomeModule has been deprecated, and we intend to remove it"`  
-`              " in a future release of Biopython. Please use the SomeOtherModule"`  
-`              " instead, as described in the Tutorial. If you would like to"`  
-`              " continue using Bio.SomeModule, please contact the Biopython"`  
-`              " developers via the mailing list.",`  
-`              DeprecationWarning)`
+```
+import warnings
+warnings.warn("Bio.SomeModule has been deprecated, and we intend to remove it"
+              " in a future release of Biopython. Please use the SomeOtherModule" 
+              " instead, as described in the Tutorial. If you would like to"
+              " continue using Bio.SomeModule, please contact the Biopython"
+              " developers via the mailing list.",
+              DeprecationWarning)
+```
 
 -   In principle, we require that two Biopython releases carrying the
     deprecation warning are made before the code can be

wiki/Documentation.md

@@ -4,8 +4,6 @@ permalink: wiki/Documentation
 layout: page
 ---
 
-#### Documentation
-
 New to Biopython? Check out the [Getting
 Started](Getting_Started "wikilink") page, or follow one of the links
 below.
@@ -32,8 +30,9 @@ below.
 -   Wiki documentation,
     -   [Seq](Seq "wikilink") and [SeqRecord](SeqRecord "wikilink")
         objects
-    -   [Bio.SeqIO](SeqIO "wikilink") - sequence input/output
+	-   [Bio.SeqIO](SeqIO "wikilink") - sequence input/output
     -   [Bio.AlignIO](AlignIO "wikilink") - alignment input/output
+	-   [Bio.Restriction](Restriction "wikilink") - using restriction enzymes
     -   [Bio.PopGen](PopGen "wikilink") - population genetics
     -   [Bio.PDB](The_Biopython_Structural_Bioinformatics_FAQ "wikilink") -
         structural bioinformatics
@@ -48,87 +47,91 @@ below.
 -   Documentation for the cluster module in Biopython. This describes
     the underlying C library and the Python interface.
 
-    [PDF](http://biopython.org/DIST/docs/cluster/cluster.pdf)
+    [PDF (2008)](http://biopython.org/DIST/docs/cluster/cluster.pdf) | 
+	[PDF (2013)](http://bonsai.hgc.jp/~mdehoon/software/cluster/cluster.pdf)
 
 -   Cookbook-style documentation:
     -   [Cookbook documentation](Category%3ACookbook "wikilink") (on
-        the wiki)
+        the wiki).
     -   The Biopython Structural Bioinformatics FAQ (i.e. how to use the
         Bio.PDB module).
-
 
-    [PDF](http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf)
-
-    -   Working with restriction enzymes.
+        [PDF](http://biopython.org/DIST/docs/tutorial/biopdb_faq.pdf)
 
+    -   [Working with restriction enzymes](Restriction "wikilink").
 
-    [HTML](http://biopython.org/DIST/docs/cookbook/Restriction.html)
 
 #### Documentation for Developers
 
 -   List of [Active projects](Active_projects "wikilink") to get
     involved with.
 -   How to [contribute code](Contributing "wikilink") to Biopython.
 -   [Deprecation policy](Deprecation_policy "wikilink")
--   Instructions for [building a release](building_a_release "wikilink")
+-   Instructions for [building a release](Building_a_release "wikilink")
     of Biopython.
--   Details about the biopython.org [website](website "wikilink").
+-   Details about the biopython.org [website](https://github.com/biopython/biopython.github.io).
 
 #### Online Course Notes
 
 -   Andrew Dalke taught an introduction to programming for
     Bioinformatics in Python class at the National Bioinformatics
     Network in South Africa.
 
-    <http://www.dalkescientific.com/writings/NBN/>
+    [html](http://www.dalkescientific.com/writings/NBN/)
 
--   Ravinder Singh and Scott Kelley teach a Bioinformatics course using
-    Biopython at the University of Colorado.
-      
-    <http://www.colorado.edu/catalog/2012-13/courses?college=ARSC&department=B-MCDB>
+-   Kristian Rother wrote a GitBook for learning Biopython with two case studies
+
+    [GitBook](https://www.gitbook.com/book/krother/biopython-tutorial/details)
 
 
 #### Papers
 
 We have a separate list of [publications citing or using
 Biopython](Publications "wikilink"). If you use Biopython in a
 scientific publication, please cite the application note
-<cite>CockEtAl2009</cite> and/or one of the other listed papers:
+([Cock *et al.*, 2009](http://dx.doi.org/10.1093/bioinformatics/btp163))
+and/or one of the other listed papers:
 
-<biblio>
+1.  Cock PA, Antao T, Chang JT, Bradman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, 
+    Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational
+	molecular biology and bioinformatics. [Bioinformatics, 25, 1422-1423](http://dx.doi.org/10.1093/bioinformatics/btp163)
 
-1.  CockEtAl2009 pmid=19304878
+    // This application note covers the whole of Biopython
 
-// This application note covers the whole of Biopython
+2.  Chapman BA and Chang JT (2000). Biopython: Python tools for computational biology.
+    [ACM SIGBIO Newsletter, 20, 15-19](http://dx.doi.org/10.1145/360262.360268).
 
-1.  ChapmanAndChang2000 Chapman BA and Chang JT. *Biopython: Python
-    tools for computational biology.* ACM SIGBIO Newsletter 2000 Aug;
-    20, 15-19. [HTML](http://biopython.org/DIST/docs/acm/ACMbiopy.html)
+	[HTML](http://biopython.org/DIST/docs/acm/ACMbiopy.html)
     | [PDF](http://biopython.org/DIST/docs/acm/ACMbiopy.pdf)
 
-// This served as the official project announcement.
+    // This served as the official project announcement.
 
-1.  HamelryckAndManderick2003 pmid=14630660
+3.  Hamelryck T and Manderick B (2003) PDB file parser and structure class implemented in Python.
+    [Bioinformatics, 22, 2308-2310](http://dx.doi.org/10.1093/bioinformatics/btg299)
 
-// The Bio.PDB module is described here.
+    // The `Bio.PDB` module is described here.
 
-1.  DeHoonEtAl2004 pmid=14871861
+4.  de Hoon MJ, Imoto S, Nolan J and Miyano S (2004) Open source clustering software.
+    [Bioinformatics, 20, 1454-1453](http://dx.doi.org/10.1093/bioinformatics/bth078)
 
-// The Bio.Cluster module is described here.
+    // The `Bio.Cluster` module is described here.
 
-1.  PritchardEtAl2006 pmid=16377612
+5.  Pritchard L, White JA, Birch PR and Toth IK (2006) GenomeDiagram: a Python package for the
+    visualization of large-scale genomic data. [Bioinformatics, 22, 616-617](http://dx.doi.org/10.1093/bioinformatics/btk021)
 
-// This describes GenomeDiagram, which has now been integrated into
-Biopython.
+    // This describes `GenomeDiagram`, which has now been integrated into Biopython.
 
-1.  CockEtAl2009b pmid=20015970
+6.  Cock PJ, Fields CJ, Goto N, Heuer ML and Rice PM (2009) The Sanger FASTQ file format for sequences with
+    quality scores, and the Solexa/Illumina FASTQ variants.
+    [Nucleic Acids Res., 38, 1767-1771](http://dx.doi.org/10.1093/nar/gkp1137)
 
-// This describes the FASTQ file format as supported in Biopython,
-BioPerl, BioRuby, BioJava and EMBOSS
+    // This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS
 
-1.  TalevichEtAl2012 pmid=22909249
+7.  Talevich E, Invergo BM, Cock PJ and Chapman BA (2012) Bio.Phylo: a unified toolkit for processing, analyzing
+    and visualizing phylogenetic trees in Biopython.
+    [BMC Bioinformatics, 13, 209](http://dx.doi.org/10.1186/1471-2105-13-209)
 
-// This describes the Bio.Phylo and Bio.Phylo.PAML modules. </biblio>
+    // This describes the `Bio.Phylo` and `Bio.Phylo.PAML modules`.
 
 #### Presentations