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Description: adjust tutorial to document muscle3 usage.
In addition to being up to date with the way of doing things for the upcoming
Debian version, this fixes the doctest failures.
Author: Étienne Mollier <emollier@debian.org>
Forwarded: no
Last-Update: 2022-12-04
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-biopython.orig/Doc/Tutorial/chapter_align.tex
+++ python-biopython/Doc/Tutorial/chapter_align.tex
@@ -1116,7 +1116,7 @@
>>> from Bio.Align.Applications import MuscleCommandline
>>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.txt")
>>> print(cline)
-muscle -in opuntia.fasta -out opuntia.txt
+muscle3 -in opuntia.fasta -out opuntia.txt
\end{minted}
Note that MUSCLE uses ``-in'' and ``-out'' but in Biopython we have to use
@@ -1133,7 +1133,7 @@
>>> from Bio.Align.Applications import MuscleCommandline
>>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clw=True)
>>> print(cline)
-muscle -in opuntia.fasta -out opuntia.aln -clw
+muscle3 -in opuntia.fasta -out opuntia.aln -clw
\end{minted}
Or, strict ClustalW output where the original ClustalW header line is
@@ -1144,7 +1144,7 @@
>>> from Bio.Align.Applications import MuscleCommandline
>>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clwstrict=True)
>>> print(cline)
-muscle -in opuntia.fasta -out opuntia.aln -clwstrict
+muscle3 -in opuntia.fasta -out opuntia.aln -clwstrict
\end{minted}
\noindent The \verb|Bio.AlignIO| module should be able to read these alignments
@@ -1174,7 +1174,7 @@
>>> from Bio.Align.Applications import MuscleCommandline
>>> muscle_cline = MuscleCommandline(input="opuntia.fasta")
>>> print(muscle_cline)
-muscle -in opuntia.fasta
+muscle3 -in opuntia.fasta
\end{minted}
If we run this via the wrapper, we get back the output as a string. In order
@@ -1254,7 +1254,7 @@
>>> from Bio.Align.Applications import MuscleCommandline
>>> muscle_cline = MuscleCommandline(clwstrict=True)
>>> print(muscle_cline)
-muscle -clwstrict
+muscle3 -clwstrict
\end{minted}
Now for the fiddly bits using the \verb|subprocess| module, stdin and stdout:
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