Mercurial > forge
changeset 11817:8e4b2cf424b2 octave-forge
bioinfo: moved to a separate mercurial repo
| author | carandraug |
|---|---|
| date | Mon, 17 Jun 2013 16:49:15 +0000 |
| parents | ef0edb527738 |
| children | e9cefd6a4c96 |
| files | main/bioinfo/COPYING main/bioinfo/DESCRIPTION main/bioinfo/inst/aa2int.m main/bioinfo/inst/aminolookup.m main/bioinfo/inst/cleave.m main/bioinfo/inst/int2aa.m main/bioinfo/inst/seqreverse.m |
| diffstat | 7 files changed, 0 insertions(+), 795 deletions(-) [+] |
line wrap: on
line diff
--- a/main/bioinfo/COPYING Mon Jun 17 16:08:09 2013 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc. - 675 Mass Ave, Cambridge, MA 02139, USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. By contrast, the GNU General Public -License is intended to guarantee your freedom to share and change free -software--to make sure the software is free for all its users. This -General Public License applies to most of the Free Software -Foundation's software and to any other program whose authors commit to -using it. (Some other Free Software Foundation software is covered by -the GNU Library General Public License instead.) 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--- a/main/bioinfo/DESCRIPTION Mon Jun 17 16:08:09 2013 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -Name: bioinfo -Version: 0.1.2 -Date: 2009-05-06 -Author: Bill Denney <bill@denney.ws> -Maintainer: Octave Community -Title: Bioinformatics -Description: Bioinformatics manipulation -Categories: Bioinformatics -Depends: octave (>= 3.0.0) -Autoload: yes -License: GPL version 2 or later -Url: http://octave.sf.net
--- a/main/bioinfo/inst/aa2int.m Mon Jun 17 16:08:09 2013 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -## Copyright (C) 2008 Bill Denney -## -## 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} {@var{sequenceint} =} aa2int (@var{sequencechar}) -## Convert amino acid characters into integers. See @code{aminolookup} -## for the listing of numbers and their corresponding characters. -## @seealso{aminolookup,int2aa,int2nt,nt2int} -## @end deftypefn - -## Author: Bill Denney <bill@denney.ws> - -function seqi = aa2int (seqc=0) - - if (! ischar (seqc)) - print_usage (); - endif - sequences = aminolookup ("code", []); - - seqi = -ones (size (seqc)); - seqc = upper (seqc); - for i = 1:numel (sequences) - seqi(sequences(i) == seqc) = i; - endfor - if any (seqi(:) < 0) - idx = find (seqi(:) < 0, 1); - error ("aa2int: unrecognised character (%s) in sequence input at position (%d)", - seqc(idx), idx) - endif - -endfunction - -## Tests -%!assert (aa2int ("a"), 1) -%!assert (aa2int ("ar"), [1 2]) -%!assert (aa2int (["ar"]'), [1;2])
--- a/main/bioinfo/inst/aminolookup.m Mon Jun 17 16:08:09 2013 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,224 +0,0 @@ -## Copyright (C) 2008 Bill Denney -## -## 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 or outputs. -## -## If called without 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 <bill@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 - 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")
--- a/main/bioinfo/inst/cleave.m Mon Jun 17 16:08:09 2013 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,86 +0,0 @@ -## Copyright (C) 2008 Bill Denney -## -## 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} {@var{fragments} =} cleave (@var{sequence}, @var{pattern}, @var{position}) -## @deftypefnx {Function File} {[@var{fragments}, @var{cuttingsites}] =} cleave (@dots{}) -## @deftypefnx {Function File} {[@var{fragments}, @var{cuttingsites}, @var{lengths}] =} cleave (@dots{}) -## @deftypefnx {Function File} {[@dots{}] =} cleave (@dots{}, "PartialDigest", @var{prob}) -## Cleave a peptide @var{sequence} using the @var{pattern} at the -## @var{position} relative to the pattern. The @var{sequence} is a -## sequence of amino acids; the @var{pattern} is a regular expression to -## find the location of the cleavage; and the @var{position} is the -## position relative to that regular expression (0 is immediately to the -## left of the first character, 1 is immediately to the right of the -## first character, @dots{}). -## -## Example regular expressions for some commone proteases are given -## below. -## -## @multitable @columnfractions .5 .3 .2 -## @item Protease @tab Peptide Pattern @tab Position -## @item Trypsin @tab [KR](?!P) @tab 1 -## @item Chymotrypsin @tab [WYF](?!P) @tab 1 -## @item Glutamine C @tab [ED](?!P) @tab 1 -## @item Lysine C @tab [K](?!P) @tab 1 -## @item Aspartic acid N @tab D @tab 1 -## @end multitable -## -## @seealso{rebasecuts, restrict, seqshowwords, regexp} -## @end deftypefn - -## Author: Bill Denney <bill@denney.ws> - -function [fragments, s, lengths] = cleave (seq, pattern, pos, varargin) - - if isstruct (seq) - seq = seq.sequence; - endif - if (rows (seq) != 1) - error ("seqreverse: the sequence must have a single row"); - endif - if (! isempty (varargin)) - ## FIXME: add support for partialdigest - error ("cleave: additional parameters are not yet supported") - endif - - s = [0 (pos - 1 + regexp (seq, pattern))]; - ## There is no cleavage at the end-- there was already a cleavage - ## there. - if (s(end) == length(seq)) - s(end) = []; - endif - fragments = cell (size (s)); - lengths = [s(2:end) length(seq)] - s; - for i = 1:numel (s) - fragments{i} = seq(s(i)+1:s(i)+lengths(i)); - endfor - -endfunction - -## Tests -%!test -%! site = [0 6 7 41 46 67 74 80 92 100]; -%! len = [6 1 34 5 21 7 6 12 8 10]; -%! frag = {"MGTGGR" "R" "GAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIR" "NNLTR" \ -%! "LHELENCSVIEGHLQILLMFK" "TRPEDFR" "DLSFPK" "LIMITDYLLLFR" \ -%! "VYGLESLK" "DLFPNLTVIR"}; -%! seq = strcat (frag{:}); -%! [tfrag, tsite, tlen] = cleave (seq, '[KR](?!P)', 1); -%! assert (tfrag, frag) -%! assert (tsite, site) -%! assert (tlen, len) -## FIXME: This needs a test for partialdigest.
--- a/main/bioinfo/inst/int2aa.m Mon Jun 17 16:08:09 2013 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -## Copyright (C) 2008 Bill Denney -## -## 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} {@var{sequencechar} =} int2aa (@var{sequenceint}) -## Convert amino acid integers into characters. See @code{aminolookup} -## for the listing of numbers and their corresponding characters. -## @seealso{aminolookup,aa2int,int2nt,nt2int} -## @end deftypefn - -## Author: Bill Denney <bill@denney.ws> - -function seqc = int2aa (seqi) - - if (! isnumeric (seqi)) - print_usage (); - endif - sequences = aminolookup ("code", []); - seqc = reshape (sequences(seqi), size (seqi)); -endfunction - -## Tests -%!assert (int2aa (1), "A") -%!assert (int2aa ([1 2]), "AR"); -%!assert (int2aa ([1;2]), ["A";"R"])
--- a/main/bioinfo/inst/seqreverse.m Mon Jun 17 16:08:09 2013 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ -## Copyright (C) 2008 Bill Denney -## -## 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} {@var{seqr} =} seqreverse (@var{seqf}) -## Reverse a nucleotide sequence. @var{seqf} can be either a numeric or -## code DNA or RNA sequence or a struct with the field sequence, and it -## will reverse the direction of the sequence. -## @seealso{seqcomplement, seqrcomplement} -## @end deftypefn - -## Author: Bill Denney <bill@denney.ws> - -function s = seqreverse (seqf) - - if isstruct (seqf) - s = seqf.sequence; - else - s = seqf; - endif - - if (rows (s) != 1) - error ("seqreverse: the sequence must have a single row"); - endif - s = fliplr (s); - if isstruct (seqf) - seqf.sequence = s; - s = seqf; - endif -endfunction - -## Tests -%!assert (seqreverse ("ATCG"), "GCTA") -%!assert (seqreverse (struct ("sequence", "ATCG")), struct ("sequence", "GCTA"));