[Biopython-dev] [Bug 2822] Bio.Application.AbstractCommandline - properties and kwargs

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2822


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
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Attachment #1291 is|0                           |1
           obsolete|                            |




------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-04 12:29 EST -------
(From update of attachment 1291)
Checked into CVS:

Checking in Tests/test_Prank_tool.py;
/home/repository/biopython/biopython/Tests/test_Prank_tool.py,v  <-- 
test_Prank_tool.py
new revision: 1.5; previous revision: 1.4
done
Checking in Tests/test_Muscle_tool.py;
/home/repository/biopython/biopython/Tests/test_Muscle_tool.py,v  <-- 
test_Muscle_tool.py
new revision: 1.7; previous revision: 1.6
done
Checking in Tests/test_Emboss.py;
/home/repository/biopython/biopython/Tests/test_Emboss.py,v  <-- 
test_Emboss.py
new revision: 1.20; previous revision: 1.19
done
Checking in Tests/test_Clustalw_tool.py;
/home/repository/biopython/biopython/Tests/test_Clustalw_tool.py,v  <-- 
test_Clustalw_tool.py
new revision: 1.13; previous revision: 1.12
done
Checking in Bio/Application/__init__.py;
/home/repository/biopython/biopython/Bio/Application/__init__.py,v  <-- 
__init__.py
new revision: 1.15; previous revision: 1.14
done
Checking in Bio/Emboss/Applications.py;
/home/repository/biopython/biopython/Bio/Emboss/Applications.py,v  <-- 
Applications.py
new revision: 1.23; previous revision: 1.22
done
Checking in Bio/AlignAce/Applications.py;
/home/repository/biopython/biopython/Bio/AlignAce/Applications.py,v  <-- 
Applications.py
new revision: 1.5; previous revision: 1.4
done
Checking in Bio/Motif/Applications/_AlignAce.py;
/home/repository/biopython/biopython/Bio/Motif/Applications/_AlignAce.py,v  <--
 _AlignAce.py
new revision: 1.3; previous revision: 1.2
done
Checking in Bio/Align/Applications/_Clustalw.py;
/home/repository/biopython/biopython/Bio/Align/Applications/_Clustalw.py,v  <--
 _Clustalw.py
new revision: 1.5; previous revision: 1.4
done
Checking in Bio/Align/Applications/_Mafft.py;
/home/repository/biopython/biopython/Bio/Align/Applications/_Mafft.py,v  <-- 
_Mafft.py
new revision: 1.4; previous revision: 1.3
done
Checking in Bio/Align/Applications/_Muscle.py;
/home/repository/biopython/biopython/Bio/Align/Applications/_Muscle.py,v  <-- 
_Muscle.py
new revision: 1.6; previous revision: 1.5
done
Checking in Bio/Align/Applications/_Prank.py;
/home/repository/biopython/biopython/Bio/Align/Applications/_Prank.py,v  <-- 
_Prank.py
new revision: 1.4; previous revision: 1.3
done

(In reply to comment #7)
> (In reply to comment #6)
> > Still need to co-ordinate with Cymon to give the Muscle wrapper a valid
> > python identifier as an alias for the -in argument, e.g. "input", because
> > we can't use just "in" as a property or keyword argument.
> 
> "input" for -in and maybe also "input1" "input2" as alternatives for -in1
> -in2, might the the way to go, and document it.

I've used "input" as the preferred alias for "-in".

Leaving this bug open to cover dealing with "switch" arguments like -kimura in
clustalw, where it makes sense to treat the value as a boolean (see dev mailing
list).

Peter


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