Mercurial > repos > vipints > rdiff

comparison rDiff/src/tools/transform_single_end_reads.m @ 0:0f80a5141704

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
version 0.3 uploaded
author vipints
date Thu, 14 Feb 2013 23:38:36 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:0f80a5141704
1 function [UNIQUE_NEW_EXONS, GRAPHNODES, ORDER_OF_GRAPHNODE, EIRS_IN_SEQ] = transform_single_end_reads(gene, SEQUENCED_LENGTH)
2 % This function calculates all regions onto which a read may fall.
3 % SEQUENCED_LENGTH is the length of a read.
4
5 SPLICINGEVENTS=gene.splicingevents;
6 SEQUENCE=gene.sequence;
7 EXONSEQUENCE=gene.exonsequence;
8
9 NB_OF_TRANS = size(EXONSEQUENCE,1);
10
11 NEWEXONS = 1:(length(SPLICINGEVENTS) - 1);
12 UNIQUE_NEW_EXONS = NEWEXONS(SEQUENCE>0);
13
14 NB_OF_EXONS = length(UNIQUE_NEW_EXONS);
15 MAX_EXON_NB_TO_POS = cumsum((NEWEXONS .* SEQUENCE) > 0);
16
17 % NB_EXONSEQUENCE is for each transcript the position in
18 % SPLICINGEVENTS where one of its exonic region starts and 0 if it
19 % is intronic
20
21 NB_EXONSEQUENCE = EXONSEQUENCE .* repmat(NEWEXONS,NB_OF_TRANS,1);
22
23 %%% This contains all exons
24 GRAPHNODES = [];
25
26 %%% This is the array where a 1 is in column j if that EIR (Exons in
27 %a region covered by a read) is contained in the transcript
28 EIRS_IN_SEQ = [];
29
30 CURRENT_NODE = 0;% To catch errors with non-initalized variable
31
32 EIR_TRANSCRIPTS = cell(1,NB_OF_TRANS);
33 ORDER_OF_GRAPHNODE = cell(1,NB_OF_TRANS);
34 LENGTHS_OF_GRAPHNODE = cell(1,NB_OF_TRANS);
35
36 SPLICING_LENGTHS = SPLICINGEVENTS(2:end) - SPLICINGEVENTS(1:end-1);
37
38 for i = 1:NB_OF_TRANS
39
40 %%% remove zero positions, adjust splicing positions
41 CURRENT_EXONS = NB_EXONSEQUENCE(i, EXONSEQUENCE(i,:) > 0);
42
43 SPLICING_CORRECT = cumsum(SPLICING_LENGTHS .* (NB_EXONSEQUENCE(i,:) == 0));
44 %SPLICING_CORRECT contains the position of SPLICINGSEQUENCE in
45 %the transcript when all introns are spliced out
46 SPLICING_CORRECT = [1, SPLICINGEVENTS(2:end) - SPLICING_CORRECT];
47
48 %This ensures that the end of the transcript is also in CURRENT_SPLICINGEVENTS
49 IDX = EXONSEQUENCE(i,:) == 1 ;
50 IDX(find(EXONSEQUENCE(i,:) == 1, 1, 'last') + 1) = true;
51 CURRENT_SPLICINGEVENTS = SPLICING_CORRECT(IDX);
52 if length(CURRENT_SPLICINGEVENTS) == 0
53 continue
54 end
55 LASTPOS = CURRENT_SPLICINGEVENTS(end);
56 if LASTPOS <= SEQUENCED_LENGTH
57 warning('CURRENT_SPLICINGEVENTS(end) > SEQUENCED_LENGTH')
58 end
59 %assert(LASTPOS > SEQUENCED_LENGTH,'CURRENT_SPLICINGEVENTS(end) > SEQUENCED_LENGTH')
60 % Calculate the positions when the EIRS can change
61
62 % Determine positions which start SEQUENCED_LENGTH positions before a splicing event
63 % defines a window of size SEQUENCED_LENGTH around the CURRENT_SPLICINGEVENTS
64 READEVENTS_START = max([CURRENT_SPLICINGEVENTS(1:end - 1) - SEQUENCED_LENGTH + 1; ones(1,length(CURRENT_SPLICINGEVENTS)-1)],[],1);
65 READEVENTS_END = min([CURRENT_SPLICINGEVENTS(2:end); repmat(LASTPOS - SEQUENCED_LENGTH,1,length(CURRENT_SPLICINGEVENTS(2:end)))],[],1);
66
67 % Calculate EIRS
68 % CHANGE_POINTS are those points in a transcript where a EIR changes, namly the splicesites of that transcript plus and
69 % minus the SEQUENCED_LENGTH - the above descibed window
70 CHANGE_POINTS = unique([READEVENTS_START, READEVENTS_END]);
71
72 for j = 1:(length(CHANGE_POINTS) - 1)
73
74 POINTS_OF_INTEREST = ( READEVENTS_START(1,:) <= CHANGE_POINTS(j)) & (READEVENTS_END(1,:) > CHANGE_POINTS(j));
75
76 % MAX_EXON_NB_TO_POS is mapping back to the unspliced coordinates
77 CURRENT_EIRS = zeros(1,NB_OF_EXONS);
78 CURRENT_EIRS( MAX_EXON_NB_TO_POS(CURRENT_EXONS(POINTS_OF_INTEREST))) = 1;
79
80 %%% Already seen such exon composition in sliding
81 %%% window?
82 [TEMP, CURRENT_NODE] = intersect(GRAPHNODES, CURRENT_EIRS, 'rows');
83 if isempty(TEMP)
84 GRAPHNODES = [GRAPHNODES; CURRENT_EIRS]; %Add Key
85 EIRS_IN_SEQ = [EIRS_IN_SEQ, zeros(NB_OF_TRANS,1)];
86 CURRENT_NODE = size(GRAPHNODES,1);
87 end
88
89 EIRS_IN_SEQ(i,CURRENT_NODE) = 1;
90 ORDER_OF_GRAPHNODE{i} = [ORDER_OF_GRAPHNODE{i}, CURRENT_NODE];
91 LENGTHS_OF_GRAPHNODE{i} = [LENGTHS_OF_GRAPHNODE{i}, [CHANGE_POINTS(j); CHANGE_POINTS(j+1)]];
92 end
93 end
94