DOC: Fix text formatting for tables in sequence subpackages (scikit-b…

…io#1957)

skbio/sequence/_dna.py

@@ -61,13 +61,13 @@ class DNA(GrammaredSequence, NucleotideMixin):
     +-----+-----------+
     |Code |Nucleobase |
     +=====+===========+
-    |`A`  |Adenine    |
+    |``A``|Adenine    |
     +-----+-----------+
-    |`C`  |Cytosine   |
+    |``C``|Cytosine   |
     +-----+-----------+
-    |`G`  |Guanine    |
+    |``G``|Guanine    |
     +-----+-----------+
-    |`T`  |Thymine    |
+    |``T``|Thymine    |
     +-----+-----------+
 
     And the following 11 degenerate characters, each of which representing 2-4
@@ -76,33 +76,33 @@ class DNA(GrammaredSequence, NucleotideMixin):
     +-----+-------------+-----------+
     |Code |Nucleobases  |Meaning    |
     +=====+=============+===========+
-    |`R`  |A or G       |Purine     |
+    |``R``|A or G       |Purine     |
     +-----+-------------+-----------+
-    |`Y`  |C or T       |Pyrimidine |
+    |``Y``|C or T       |Pyrimidine |
     +-----+-------------+-----------+
-    |`S`  |G or C       |Strong     |
+    |``S``|G or C       |Strong     |
     +-----+-------------+-----------+
-    |`W`  |A or T       |Weak       |
+    |``W``|A or T       |Weak       |
     +-----+-------------+-----------+
-    |`K`  |G or T       |Keto       |
+    |``K``|G or T       |Keto       |
     +-----+-------------+-----------+
-    |`M`  |A or C       |Amino      |
+    |``M``|A or C       |Amino      |
     +-----+-------------+-----------+
-    |`B`  |C, G or T    |Not A      |
+    |``B``|C, G or T    |Not A      |
     +-----+-------------+-----------+
-    |`D`  |A, G or T    |Not C      |
+    |``D``|A, G or T    |Not C      |
     +-----+-------------+-----------+
-    |`H`  |A, C or T    |Not G      |
+    |``H``|A, C or T    |Not G      |
     +-----+-------------+-----------+
-    |`V`  |A, C or G    |Not T      |
+    |``V``|A, C or G    |Not T      |
     +-----+-------------+-----------+
-    |`N`  |A, C, G or T |Any        |
+    |``N``|A, C, G or T |Any        |
     +-----+-------------+-----------+
 
-    Plus two gap characters: `-` and `.`.
+    Plus two gap characters: ``-`` and ``.``.
 
     Characters other than the above 17 are not allowed. If you intend to use
-    additional characters to represent non-canonical nucleobases, such as `I`
+    additional characters to represent non-canonical nucleobases, such as ``I``
     (Inosine), you may create a custom alphabet using ``GrammaredSequence``.
     Directly modifying the alphabet of ``DNA`` may break methods that rely on
     the IUPAC alphabet.

skbio/sequence/_protein.py

@@ -59,45 +59,45 @@ class Protein(GrammaredSequence):
     +-----+---------+--------------+
     |Code |3-letter |Amino acid    |
     +=====+=========+==============+
-    |`A`  |Ala      |Alanine       |
+    |``A``|Ala      |Alanine       |
     +-----+---------+--------------+
-    |`C`  |Cys      |Cysteine      |
+    |``C``|Cys      |Cysteine      |
     +-----+---------+--------------+
-    |`D`  |Asp      |Aspartic acid |
+    |``D``|Asp      |Aspartic acid |
     +-----+---------+--------------+
-    |`E`  |Glu      |Glutamic acid |
+    |``E``|Glu      |Glutamic acid |
     +-----+---------+--------------+
-    |`F`  |Phe      |Phenylalanine |
+    |``F``|Phe      |Phenylalanine |
     +-----+---------+--------------+
-    |`G`  |Gly      |Glycine       |
+    |``G``|Gly      |Glycine       |
     +-----+---------+--------------+
-    |`H`  |His      |Histidine     |
+    |``H``|His      |Histidine     |
     +-----+---------+--------------+
-    |`I`  |Ile      |Isoleucine    |
+    |``I``|Ile      |Isoleucine    |
     +-----+---------+--------------+
-    |`K`  |Lys      |Lysine        |
+    |``K``|Lys      |Lysine        |
     +-----+---------+--------------+
-    |`L`  |Leu      |Leucine       |
+    |``L``|Leu      |Leucine       |
     +-----+---------+--------------+
-    |`M`  |Met      |Methionine    |
+    |``M``|Met      |Methionine    |
     +-----+---------+--------------+
-    |`N`  |Asn      |Asparagine    |
+    |``N``|Asn      |Asparagine    |
     +-----+---------+--------------+
-    |`P`  |Pro      |Proline       |
+    |``P``|Pro      |Proline       |
     +-----+---------+--------------+
-    |`Q`  |Gln      |Glutamine     |
+    |``Q``|Gln      |Glutamine     |
     +-----+---------+--------------+
-    |`R`  |Arg      |Arginine      |
+    |``R``|Arg      |Arginine      |
     +-----+---------+--------------+
-    |`S`  |Ser      |Serine        |
+    |``S``|Ser      |Serine        |
     +-----+---------+--------------+
-    |`T`  |Thr      |Threonine     |
+    |``T``|Thr      |Threonine     |
     +-----+---------+--------------+
-    |`V`  |Val      |Valine        |
+    |``V``|Val      |Valine        |
     +-----+---------+--------------+
-    |`W`  |Trp      |Tryptophan    |
+    |``W``|Trp      |Tryptophan    |
     +-----+---------+--------------+
-    |`Y`  |Tyr      |Tyrosine      |
+    |``Y``|Tyr      |Tyrosine      |
     +-----+---------+--------------+
 
     And the following four degenerate characters, each of which representing
@@ -106,27 +106,27 @@ class Protein(GrammaredSequence):
     +-----+---------+------------+
     |Code |3-letter |Amino acids |
     +=====+=========+============+
-    |`B`  |Asx      |D or N      |
+    |``B``|Asx      |D or N      |
     +-----+---------+------------+
-    |`Z`  |Glx      |E or Q      |
+    |``Z``|Glx      |E or Q      |
     +-----+---------+------------+
-    |`J`  |Xle      |I or L      |
+    |``J``|Xle      |I or L      |
     +-----+---------+------------+
-    |`X`  |Xaa      |All 20      |
+    |``X``|Xaa      |All 20      |
     +-----+---------+------------+
 
-    Plus one stop character: `*` (Ter), and two gap characters: `-` and `.`.
+    Plus one stop character: ``*`` (Ter), and two gap characters: ``-`` and ``.``.
 
     Characters other than the above 27 are not allowed. If you intend to use
-    additional characters to represent non-canonical amino acids, such as `U`
-    (Sec, Selenocysteine) and `O` (Pyl, Pyrrolysine), you may create a custom
+    additional characters to represent non-canonical amino acids, such as ``U``
+    (Sec, Selenocysteine) and ``O`` (Pyl, Pyrrolysine), you may create a custom
     alphabet using ``GrammaredSequence``. Directly modifying the alphabet of
     ``Protein`` may break functions that rely on the IUPAC alphabet.
 
     It should be noted that some functions do not support certain characters.
-    For example, the BLOSUM and PAM substitution matrices do not support `J`
+    For example, the BLOSUM and PAM substitution matrices do not support ``J``
     (Xle). In such circumstances, unsupported characters will be replaced with
-    `X` to represent any of the canonical amino acids.
+    ``X`` to represent any of the canonical amino acids.
 
     References
     ----------

skbio/sequence/_rna.py

@@ -60,19 +60,19 @@ class RNA(GrammaredSequence, NucleotideMixin):
     +-----+-----------+
     |Code |Nucleobase |
     +=====+===========+
-    |`A`  |Adenine    |
+    |``A``|Adenine    |
     +-----+-----------+
-    |`C`  |Cytosine   |
+    |``C``|Cytosine   |
     +-----+-----------+
-    |`G`  |Guanine    |
+    |``G``|Guanine    |
     +-----+-----------+
-    |`U`  |Uracil     |
+    |``U``|Uracil     |
     +-----+-----------+
 
-    Plus 11 degenerate characters: `R`, `Y`, `S`, `W`, `K`, `M`, `B`, `D`, `H`,
-    `V` and `N`, and two gap characters: `-` and `.`. The definitions of
-    degenerate characters are provided in ``DNA``, in which `T` should be
-    replaced with `U` for RNA sequences.
+    Plus 11 degenerate characters: ``R``, ``Y``, ``S``, ``W``, ``K``, ``M``, ``B``,
+    ``D``, ``H``, ``V`` and ``N``, and two gap characters: ``-`` and ``.``. The
+    definitions of degenerate characters are provided in ``DNA``, in which ``T`` should
+    be replaced with ``U`` for RNA sequences.
 
     Characters other than the above 17 are not allowed. To include additional
     characters, you may create a custom alphabet using ``GrammaredSequence``.