Mercurial > repos > vipints > deseq_hts
annotate deseq-hts_2.0/src/mask_dubl.m @ 11:cec4b4fb30be draft default tip
DEXSeq version 1.6 added
author | vipints <vipin@cbio.mskcc.org> |
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date | Tue, 08 Oct 2013 08:22:45 -0400 |
parents | 2fe512c7bfdf |
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1 function [new_genes]=mask_dubl(genes,THRESH); |
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2 |
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3 CHROMOSOMES={}; |
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4 COUNTER=1; |
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5 for i=1:size(genes,2) |
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6 CHROMOSOMES{COUNTER}=genes(i).chr; |
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7 COUNTER=COUNTER+1; |
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8 end |
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9 CHROMOSOMES=unique(CHROMOSOMES); |
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10 |
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11 |
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12 INFO=zeros(size(genes,2),4); |
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13 for i=1:size(genes,2) |
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14 CHR_VAL=0; |
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15 for chr= 1:length(CHROMOSOMES) |
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16 if strcmp(genes(i).chr,CHROMOSOMES(chr)) |
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17 CHR_VAL=chr; |
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18 end |
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19 end |
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20 INFO(i,:)=[i,genes(i).start,genes(i).stop, CHR_VAL]; |
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21 end |
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22 |
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23 COUNTER=1; |
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24 new_genes=genes; |
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25 for chr= 1:length(CHROMOSOMES) |
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26 GENES_ON_CHR=INFO(INFO(:,4)==chr,:); |
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27 [TEMP,POS]=sort(GENES_ON_CHR(:,2)); |
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28 GENES_ON_CHR=GENES_ON_CHR(POS,:); |
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29 STARTS=GENES_ON_CHR(:,2); |
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30 STOPS=GENES_ON_CHR(:,3); |
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31 for i=1:(size(GENES_ON_CHR,1)) |
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32 MIN_START=find(STOPS>=STARTS(i),1,'first'); |
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33 MAX_STOP=find(STARTS<=STOPS(i),1,'last'); |
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34 if MIN_START==i |
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35 MIN_START=[]; |
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36 end |
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37 if MAX_STOP==i |
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38 MAX_STOP=[]; |
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39 end |
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40 EXONS=[]; |
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41 if not (isempty(MIN_START)) |
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42 for CURR=MIN_START:(i-1) |
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43 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).transcripts))) |
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44 for tra=1:size(genes(GENES_ON_CHR(CURR,1)).transcripts,2) |
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45 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).exons))) |
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46 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).exons{tra}]; |
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47 else |
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48 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop]; |
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49 end |
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50 end |
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51 else |
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52 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop]; |
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53 end |
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54 end |
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55 end |
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56 if not (isempty(MAX_STOP)) |
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57 for CURR=(i+1):MAX_STOP |
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58 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).transcripts))) |
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59 for tra=1:size(genes(GENES_ON_CHR(CURR,1)).transcripts,2) |
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60 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).exons))) |
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61 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).exons{tra}]; |
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62 else |
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63 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop]; |
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64 end |
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65 end |
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66 else |
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67 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop]; |
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68 end |
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69 |
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70 end |
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71 end |
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72 if not (isempty([MAX_STOP,MIN_START])) |
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73 EXONS=EXONS(EXONS(:,2)>=STARTS(i),:); |
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74 EXONS=EXONS(EXONS(:,1)<=STOPS(i),:); |
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75 new_genes(GENES_ON_CHR(i,1)).non_unique_regions=EXONS; |
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76 else |
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77 new_genes(GENES_ON_CHR(i,1)).non_unique_regions=[]; |
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78 end |
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79 end |
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80 COUNTER=COUNTER+1; |
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81 end |