I don't personally do bioinformatics, but since the package
corresponds to (a small part of) a Matlab toolbox it would be nice to
keep it for possible future elaboration. I tweaked aminolookup with
the result that it passes all tests in Octave 3.2.4 (see below; the
error is the one discussed here:
http://octave.1599824.n4.nabble.com/octave-3-2-4-sprintf-error-message-td3019273.html
). The other functions in the package also pass all tests.
Nir
diff --suppress-common-lines -d --speed-large-files
--suppress-blank-empty
/usr/share/octave/packages/3.2/bioinfo-0.1.2/aminolookup.m
aminolookup.m
1a2
> ## Nir Krakauer, 2011: modified to work in Octave 3.2
39c40
< ## any arguments or outputs.
---
> ## any arguments.
41c42
< ## If called without zero inputs, this will display the mapping between
---
> ## If called with zero inputs, this will display the mapping between
112a114,115
> result = n;
> return
183c186
< result = sprintf ("%s %s %s", data.code(value),
data.abbr(value), data.name(value));
---
> result = sprintf ("%s %s %s", data.code(value), data.abbr{value},
> data.name{value});
____________________________________________________________
## Copyright (C) 2008 Bill Denney
## Nir Krakauer, 2011: modified to work in Octave 3.2
##
## This software is free software; you can redistribute it and/or modify it
## under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or (at
## your option) any later version.
##
## This software is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this software; see the file COPYING. If not, see
## <http://www.gnu.org/licenses/>.
## -*- texinfo -*-
## @deftypefn {Function File} {} aminolookup ()
## @deftypefnx {Function File} {@var{aminodesc} =} aminolookup (@var{seq})
## @deftypefnx {Function File} {@var{aminodesc} =} aminolookup
(@var{searchtype}, @var{seq})
## Convert between amino acid representations. The types of input are
##
## @itemize @bullet
## @item Name
##
## The amino acid name
## @item Code
##
## The amino acid single letter code
## @item Abbreviation
##
## The three letter abbreviation for the amino acid
## @item Integer
##
## The number representation of the amino acid
## @end itemize
##
## To see the full list of each of the above, run this function without
## any arguments.
##
## If called with zero inputs, this will display the mapping between
## the above types. If called with one input, it will convert to code
by default.
## @seealso{aa2int,int2aa,int2nt,nt2int}
## @end deftypefn
## Author: Bill Denney <b...@denney.ws>
function result = aminolookup (varargin)
persistent data
if isempty (data)
data.code = "ARNDCQEGHILKMFPSTWYVBZX*-";
data.num = 1:25;
data.abbr = {"Ala" "Arg" "Asn" "Asp" "Cys" "Gln" "Glu" "Gly" "His" \
"Ile" "Leu" "Lys" "Met" "Phe" "Pro" "Ser" "Thr" "Trp" \
"Tyr" "Val" "Asx" "Glx" "Xaa" "END" "GAP"};
data.name = cell (numel (data.code), 3);
data.name(:,1) = {"Alanine" "Arginine" "Asparagine" "Aspartic acid" \
"Cysteine" "Glutamine" "Glutamic acid" "Glycine" \
"Histidine" "Isoleucine" "Leucine" "Lysine" \
"Methionine" "Phenylalanine" "Proline" "Serine" \
"Threonine" "Tryptophan" "Tyrosine" "Valine" \
"Asparagine" "Glutamine" "Any amino acid" \
"Termination codon (translation stop)" \
"Gap of unknown length"}';
## Alternate names
data.name{4,2} = "Aspartate";
data.name{7,2} = "Glutamate";
data.name{21,2} = "Aspartic acid";
data.name{22,2} = "Glutamic acid";
data.name{21,3} = "Aspartate";
data.name{22,3} = "Glutamate";
for i = 1:numel (data.name)
if isempty (data.name{i})
data.name{i} = "";
endif
endfor
data.seq = {"GCU GCC GCA GCG" "CGU CGC CGA CGG AGA AGG" "AAU AAC" \
"GAU GAC" "UGU UGC" "CAA CAG" "GAA GAG" \
"GGU GGC GGA GGG" "CAU CAC" "AUU AUC AUA" \
"UUA UUG CUU CUC CUA CUG" "AAA AAG" "AUG" "UUU UUC" \
"CCU CCC CCA CCG" "UCU UCC UCA UCG AGU AGC" \
"ACU ACC ACA ACG" "UGG" "UAU UAC" "GUU GUC GUA GUG" \
"AAU AAC GAU GAC" "CAA CAG GAA GAG" "All codons" \
"UAA UAG UGA" "NA"};
endif
searchtype = "";
value = "";
if (nargin == 0)
n = cell (rows (data.name), 4);
n(:,1) = data.name(:,1);
for i = 1:rows (data.name)
for j = 2:columns (data.name)
if (! isempty (data.name{i,j}))
n{i,1} = sprintf ("%s or %s", n{i,1}, data.name{i,j});
endif
endfor
n{i,2} = num2str (i);
n{i,3} = data.code(i);
n{i,4} = data.seq{i};
endfor
s = max (cellfun (@numel, n));
fmt = sprintf ("%%-%ds ", s(1), s(2), s(3), s(4));
for i = 1:rows (n)
printf ([fmt "\n"], n{i,:});
endfor
result = n;
return
elseif (nargin == 1)
showmany = 1;
if isnumeric (varargin{1})
## this is an extension of the matlab options
searchtype = "integer";
elseif ischar (varargin{1})
if ((mod (numel (varargin{1}), 3) == 0) &&
(find (isupper (varargin{1})) == 1:3:numel (varargin{1})))
## if the number of characters is divisible by 3 and exactly
## every third character is upper case
searchtype = "abbreviation";
else
searchtype = "code";
endif
endif
value = varargin{1};
else
showmany = 0;
searchtype = lower (varargin{1});
value = varargin{2};
endif
if (rows (value) > 1)
error ("aminolookup: value may only be one row")
endif
if (showmany == 1)
## we need to convert many inputs into one output. First convert
## the input value into the integer form.
switch lower (searchtype)
case "code"
value = upper (value);
newvalue = -ones (size (value));
for i = 1:numel (data.code)
newvalue(value(:) == data.code(i)) = i;
endfor
outtype = "abbreviation";
case "abbreviation"
newvalue = -ones (1, numel (value)/3);
for i = 1:3:numel (value)
newvalue((i-1)/3+1) = find (strcmp (value(i:i+2), data.abbr), 1);
endfor
outtype = "code";
case "integer"
newvalue = value;
outtype = "code";
otherwise
error (["aninolookup: cannot convert multiple arguments of any type\n"
"but code, abbreviation, or integer"]);
endswitch
if (any (newvalue(:)) < 0)
idx = find ((newvalue < 0) | (newvalue > numel (data.num)), 1);
error ("aminolookup: unrecognised symbol in input at position %d", idx);
endif
switch outtype
case "code"
result = data.code(newvalue);
case "abbreviation"
result = strcat(data.abbr{newvalue});
otherwise
error ("aminolookup: invalid output type")
endswitch
elseif (showmany == 0)
## we're only showing one value
switch lower (searchtype)
case "integer"
if isempty (value)
result = ints;
else
result = sprintf ("%s %s %s", data.code(value),
data.abbr{value}, data.name{value});
endif
case "code"
if isempty (value)
result = data.code;
else
idx = find (lower (value) == lower(data.code), 1);
result = sprintf ("%s %s", data.abbr{idx}, data.name{idx});
endif
case "abbreviation"
if isempty (value)
result = data.abbr;
else
idx = find (strcmpi (value, data.abbr));
result = sprintf ("%s %s", data.code(idx), data.name{idx});
endif
case "name"
if isempty (value)
result = data.name;
else
[idx whocares] = find (strcmpi (value, data.name), 1);
result = sprintf ("%s %s", data.code(idx), data.abbr{idx});
endif
otherwise
error ("aminolookup: invalid search type, %s", searchtype)
endswitch
endif
endfunction
## Tests
%!shared code, abbr, ints
%! code = "MWKQAEDIRDIYDF";
%! abbr = "MetTrpLysGlnAlaGluAspIleArgAspIleTyrAspPhe";
%! ints = [13 18 12 6 1 7 4 10 2 4 10 19 4 14];
%!assert (aminolookup(code), abbr)
%!assert (aminolookup(abbr), code)
%!assert (aminolookup(ints), code)
%!assert (aminolookup("Code", "R"), "Arg Arginine")
%!assert (aminolookup("Integer", 1), "A Ala Alanine")
%!assert (aminolookup("Abbreviation", "asn"), "N Asparagine")
%!assert (aminolookup("Name", "proline"), "P Pro")
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