Mercurial > repos > davidvanzessen > argalaxy_tools

annotate imgt_loader/imgt_loader.r @ 57:33412e85e669 draft

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"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
author rhpvorderman
date Wed, 02 Feb 2022 10:50:01 +0000
parents 81b3eb11ed2c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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54
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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1 args <- commandArgs(trailingOnly = TRUE)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
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2 options(show.error.locations = TRUE)
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3
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4 summ.file = args[1]
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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5 sequences.file = args[2]
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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6 aa.file = args[3]
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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7 junction.file = args[4]
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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8 gapped.aa.file = args[5]
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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9 out.file = args[6]
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10
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11 print(summ.file)
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12 print(out.file)
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13
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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14 summ = read.table(summ.file, sep="\t", header=T, quote="", fill=T)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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15 sequences = read.table(sequences.file, sep="\t", header=T, quote="", fill=T)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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16 aa = read.table(aa.file, sep="\t", header=T, quote="", fill=T)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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17 gapped.aa = read.table(gapped.aa.file, sep="\t", header=T, quote="", fill=T)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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18 junction = read.table(junction.file, sep="\t", header=T, quote="", fill=T)
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19
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20 print(paste("nrow(summ)", nrow(summ)))
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21
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22 write.table(summ, out.file, sep="\t", quote=F, row.names=F, col.names=T)
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23
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24 fix_column_names = function(df){
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
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25 if("V.DOMAIN.Functionality" %in% names(df)){
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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26 names(df)[names(df) == "V.DOMAIN.Functionality"] = "Functionality"
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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27 print("found V.DOMAIN.Functionality, changed")
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28 }
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29 if("V.DOMAIN.Functionality.comment" %in% names(df)){
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30 names(df)[names(df) == "V.DOMAIN.Functionality.comment"] = "Functionality.comment"
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31 print("found V.DOMAIN.Functionality.comment, changed")
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32 }
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33 return(df)
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34 }
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35
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36 print_missing_columns = function(df, cols, label=""){
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
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37 cols_in_df = cols %in% names(df)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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38 if(sum(!cols_in_df) > 0){
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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39 print("Columns are missing from summary file, don't have:")
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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40 print(cols[!cols_in_df])
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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41 } else {
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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42 print(paste("No missing columns for", label))
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43 }
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44 }
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45
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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46 summ = fix_column_names(summ)
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47 sequences = fix_column_names(sequences)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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48 aa = fix_column_names(aa)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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49 gapped.aa = fix_column_names(gapped.aa)
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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50 junction = fix_column_names(junction)
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51
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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52 print(paste("nrow(summ)", nrow(summ)))
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53
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54 old_summary_columns=c('Sequence.ID','JUNCTION.frame','V.GENE.and.allele','D.GENE.and.allele','J.GENE.and.allele','CDR1.IMGT.length','CDR2.IMGT.length','CDR3.IMGT.length','Orientation')
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55 old_sequence_columns=c('CDR1.IMGT','CDR2.IMGT','CDR3.IMGT')
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56 old_junction_columns=c('JUNCTION')
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57
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58 added_summary_columns=c('Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence')
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59 added_sequence_columns=c('FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT')
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60
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61 added_junction_columns=c('P3.V.nt.nb','N.REGION.nt.nb','N1.REGION.nt.nb','P5.D.nt.nb','P3.D.nt.nb','N2.REGION.nt.nb','P5.J.nt.nb','X3.V.REGION.trimmed.nt.nb','X5.D.REGION.trimmed.nt.nb','X3.D.REGION.trimmed.nt.nb','X5.J.REGION.trimmed.nt.nb','N.REGION','N1.REGION','N2.REGION')
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62 added_junction_columns=c(added_junction_columns, 'P5.D1.nt.nb', 'P3.D1.nt.nb', 'N2.REGION.nt.nb', 'P5.D2.nt.nb', 'P3.D2.nt.nb', 'N3.REGION.nt.nb', 'P5.D3.nt.nb', 'P3.D2.nt.nb', 'N4.REGION.nt.nb', 'X5.D1.REGION.trimmed.nt.nb', 'X3.D1.REGION.trimmed.nt.nb', 'X5.D2.REGION.trimmed.nt.nb', 'X3.D2.REGION.trimmed.nt.nb', 'X5.D3.REGION.trimmed.nt.nb', 'X3.D3.REGION.trimmed.nt.nb', 'D.REGION.nt.nb', 'D1.REGION.nt.nb', 'D2.REGION.nt.nb', 'D3.REGION.nt.nb')
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63
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64 minimum_columns=c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")
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65 print_missing_columns(summ, minimum_columns)
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66 out=summ[,minimum_columns]
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67
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68 print(paste("nrow(summ)", nrow(summ)))
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69 print(paste("nrow(aa)", nrow(aa)))
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70
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71 out[,"CDR1.Seq"] = aa[,"CDR1.IMGT"]
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72 out[,"CDR1.Length"] = summ[,"CDR1.IMGT.length"]
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73
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74 out[,"CDR2.Seq"] = aa[,"CDR2.IMGT"]
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75 out[,"CDR2.Length"] = summ[,"CDR2.IMGT.length"]
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76
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77 out[,"CDR3.Seq"] = gapped.aa[,"CDR3.IMGT"]
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78 out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"]
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79
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80 out[,"CDR3.IMGT"] = out[,"CDR3.Seq"]
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81
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82 out[,"CDR3.Seq.DNA"] = sequences[,"CDR3.IMGT"]
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83 out[,"CDR3.Length.DNA"] = nchar(as.character(out[,"CDR3.Seq.DNA"]))
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84 out[,"Strand"] = summ[,"Orientation"]
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85 out[,"CDR3.Found.How"] = "a"
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86
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87 out[,added_summary_columns] = summ[,added_summary_columns]
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88
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89 out[,added_sequence_columns] = aa[,added_sequence_columns]
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90
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91 out[,added_junction_columns] = junction[,added_junction_columns]
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92
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93 out[,"Top V Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"]))
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94 out[,"Top D Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"]))
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95 out[,"Top J Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"]))
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96
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97 out = out[!grepl("Less than", summ[,"V.GENE.and.allele"]),]
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98 out = out[!grepl("Less than", summ[,"D.GENE.and.allele"]),]
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99 out = out[!grepl("Less than", summ[,"J.GENE.and.allele"]),]
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100
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101 out = out[,c('Sequence.ID','JUNCTION.frame','Top V Gene','Top D Gene','Top J Gene','CDR1.Seq','CDR1.Length','CDR2.Seq','CDR2.Length','CDR3.Seq','CDR3.Length','CDR3.Seq.DNA','CDR3.Length.DNA','Strand','CDR3.Found.How','Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence','FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT','P3.V.nt.nb','N.REGION.nt.nb','N1.REGION.nt.nb','P5.D.nt.nb','P3.D.nt.nb','N2.REGION.nt.nb','P5.J.nt.nb','X3.V.REGION.trimmed.nt.nb','X5.D.REGION.trimmed.nt.nb','X3.D.REGION.trimmed.nt.nb','X5.J.REGION.trimmed.nt.nb','N.REGION','N1.REGION','N2.REGION', 'P5.D1.nt.nb', 'P3.D1.nt.nb', 'N2.REGION.nt.nb', 'P5.D2.nt.nb', 'P3.D2.nt.nb', 'N3.REGION.nt.nb', 'P5.D3.nt.nb', 'P3.D2.nt.nb', 'N4.REGION.nt.nb', 'X5.D1.REGION.trimmed.nt.nb', 'X3.D1.REGION.trimmed.nt.nb', 'X5.D2.REGION.trimmed.nt.nb', 'X3.D2.REGION.trimmed.nt.nb', 'X5.D3.REGION.trimmed.nt.nb', 'X3.D3.REGION.trimmed.nt.nb', 'D.REGION.nt.nb', 'D1.REGION.nt.nb', 'D2.REGION.nt.nb', 'D3.REGION.nt.nb')]
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102
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103 names(out) = c('ID','VDJ Frame','Top V Gene','Top D Gene','Top J Gene','CDR1 Seq','CDR1 Length','CDR2 Seq','CDR2 Length','CDR3 Seq','CDR3 Length','CDR3 Seq DNA','CDR3 Length DNA','Strand','CDR3 Found How','Functionality','V-REGION identity %','V-REGION identity nt','D-REGION reading frame','AA JUNCTION','Functionality comment','Sequence','FR1-IMGT','FR2-IMGT','FR3-IMGT','CDR3-IMGT','JUNCTION','J-REGION','FR4-IMGT','P3V-nt nb','N-REGION-nt nb','N1-REGION-nt nb','P5D-nt nb','P3D-nt nb','N2-REGION-nt nb','P5J-nt nb','3V-REGION trimmed-nt nb','5D-REGION trimmed-nt nb','3D-REGION trimmed-nt nb','5J-REGION trimmed-nt nb','N-REGION','N1-REGION','N2-REGION', 'P5.D1.nt.nb', 'P3.D1.nt.nb', 'N2.REGION.nt.nb', 'P5.D2.nt.nb', 'P3.D2.nt.nb', 'N3.REGION.nt.nb', 'P5.D3.nt.nb', 'P3.D2.nt.nb', 'N4.REGION.nt.nb', 'X5.D1.REGION.trimmed.nt.nb', 'X3.D1.REGION.trimmed.nt.nb', 'X5.D2.REGION.trimmed.nt.nb', 'X3.D2.REGION.trimmed.nt.nb', 'X5.D3.REGION.trimmed.nt.nb', 'X3.D3.REGION.trimmed.nt.nb', 'D.REGION.nt.nb', 'D1.REGION.nt.nb', 'D2.REGION.nt.nb', 'D3.REGION.nt.nb')
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104
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105 out[,"VDJ Frame"] = as.character(out[,"VDJ Frame"])
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106 fltr = out[,"VDJ Frame"] == "in-frame"
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107 if(any(fltr, na.rm=T)){
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108 out[fltr, "VDJ Frame"] = "In-frame"
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109 }
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110 fltr = out[,"VDJ Frame"] == "null"
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111 if(any(fltr, na.rm = T)){
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112 out[fltr, "VDJ Frame"] = "Out-of-frame"
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113 }
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114 fltr = out[,"VDJ Frame"] == "out-of-frame"
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115 if(any(fltr, na.rm = T)){
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116 out[fltr, "VDJ Frame"] = "Out-of-frame"
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117 }
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118 fltr = out[,"VDJ Frame"] == ""
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119 if(any(fltr, na.rm = T)){
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120 out[fltr, "VDJ Frame"] = "Out-of-frame"
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121 }
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122
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123 for(col in c('Top V Gene','Top D Gene','Top J Gene')){
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124 out[,col] = as.character(out[,col])
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125 fltr = out[,col] == ""
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126 fltr[is.na(fltr)] = T
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127 if(any(fltr, na.rm = T)){
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128 out[fltr,col] = "NA"
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129 }
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130 }
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131
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132 write.table(out, out.file, sep="\t", quote=F, row.names=F, col.names=T)