Mercurial > repos > rhpvorderman > shm_csr

comparison imgt_loader.r @ 0:64d74ba01a7c draft

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"planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
author rhpvorderman
date Wed, 27 Oct 2021 12:34:47 +0000
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-1:000000000000 0:64d74ba01a7c
1 args <- commandArgs(trailingOnly = TRUE)
2
3 summ.file = args[1]
4 aa.file = args[2]
5 junction.file = args[3]
6 out.file = args[4]
7
8 summ = read.table(summ.file, sep="\t", header=T, quote="", fill=T)
9 aa = read.table(aa.file, sep="\t", header=T, quote="", fill=T)
10 junction = read.table(junction.file, sep="\t", header=T, quote="", fill=T)
11
12 fix_column_names = function(df){
13 if("V.DOMAIN.Functionality" %in% names(df)){
14 names(df)[names(df) == "V.DOMAIN.Functionality"] = "Functionality"
15 print("found V.DOMAIN.Functionality, changed")
16 }
17 if("V.DOMAIN.Functionality.comment" %in% names(df)){
18 names(df)[names(df) == "V.DOMAIN.Functionality.comment"] = "Functionality.comment"
19 print("found V.DOMAIN.Functionality.comment, changed")
20 }
21 return(df)
22 }
23
24 summ = fix_column_names(summ)
25 aa = fix_column_names(aa)
26 junction = fix_column_names(junction)
27
28 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')
29 old_sequence_columns=c('CDR1.IMGT','CDR2.IMGT','CDR3.IMGT')
30 old_junction_columns=c('JUNCTION')
31
32 added_summary_columns=c('Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence')
33 added_sequence_columns=c('FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT')
34
35 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')
36 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')
37
38 out=summ[,c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")]
39
40 out[,"CDR1.Seq"] = aa[,"CDR1.IMGT"]
41 out[,"CDR1.Length"] = summ[,"CDR1.IMGT.length"]
42
43 out[,"CDR2.Seq"] = aa[,"CDR2.IMGT"]
44 out[,"CDR2.Length"] = summ[,"CDR2.IMGT.length"]
45
46 out[,"CDR3.Seq"] = aa[,"CDR3.IMGT"]
47 out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"]
48
49 out[,"CDR3.Seq.DNA"] = junction[,"JUNCTION"]
50 out[,"CDR3.Length.DNA"] = nchar(as.character(junction[,"JUNCTION"]))
51 out[,"Strand"] = summ[,"Orientation"]
52 out[,"CDR3.Found.How"] = "a"
53
54 out[,added_summary_columns] = summ[,added_summary_columns]
55
56 out[,added_sequence_columns] = aa[,added_sequence_columns]
57
58 out[,added_junction_columns] = junction[,added_junction_columns]
59
60 out[,"Top V Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"]))
61 out[,"Top D Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"]))
62 out[,"Top J Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"]))
63
64 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')]
65
66 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')
67
68 out[,"VDJ Frame"] = as.character(out[,"VDJ Frame"])
69
70 fltr = out[,"VDJ Frame"] == "in-frame"
71 if(any(fltr, na.rm = T)){
72 out[fltr, "VDJ Frame"] = "In-frame"
73 }
74
75 fltr = out[,"VDJ Frame"] == "null"
76 if(any(fltr, na.rm = T)){
77 out[fltr, "VDJ Frame"] = "Out-of-frame"
78 }
79
80 fltr = out[,"VDJ Frame"] == "out-of-frame"
81 if(any(fltr, na.rm = T)){
82 out[fltr, "VDJ Frame"] = "Out-of-frame"
83 }
84
85 fltr = out[,"VDJ Frame"] == ""
86 if(any(fltr, na.rm = T)){
87 out[fltr, "VDJ Frame"] = "Out-of-frame"
88 }
89
90 for(col in c('Top V Gene','Top D Gene','Top J Gene')){
91 out[,col] = as.character(out[,col])
92 fltr = out[,col] == ""
93 if(any(fltr, na.rm = T)){
94 out[fltr,col] = "NA"
95 }
96 }
97
98 write.table(out, out.file, sep="\t", quote=F, row.names=F, col.names=T)