Mercurial > repos > davidvanzessen > argalaxy_tools
comparison imgt_loader/imgt_loader.r @ 0:afe85eb6572e draft
Uploaded
author | davidvanzessen |
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date | Mon, 29 Aug 2016 05:41:20 -0400 |
parents | |
children | 9185c3dfc679 |
comparison
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-1:000000000000 | 0:afe85eb6572e |
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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 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') | |
13 old_sequence_columns=c('CDR1.IMGT','CDR2.IMGT','CDR3.IMGT') | |
14 old_junction_columns=c('JUNCTION') | |
15 | |
16 added_summary_columns=c('Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence') | |
17 added_sequence_columns=c('FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT') | |
18 | |
19 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') | |
20 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') | |
21 | |
22 out=summ[,c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")] | |
23 | |
24 out[,"CDR1.Seq"] = aa[,"CDR1.IMGT"] | |
25 out[,"CDR1.Length"] = summ[,"CDR1.IMGT.length"] | |
26 | |
27 out[,"CDR2.Seq"] = aa[,"CDR2.IMGT"] | |
28 out[,"CDR2.Length"] = summ[,"CDR2.IMGT.length"] | |
29 | |
30 out[,"CDR3.Seq"] = aa[,"CDR3.IMGT"] | |
31 out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"] | |
32 | |
33 out[,"CDR3.Seq.DNA"] = junction[,"JUNCTION"] | |
34 out[,"CDR3.Length.DNA"] = nchar(as.character(junction[,"JUNCTION"])) | |
35 out[,"Strand"] = summ[,"Orientation"] | |
36 out[,"CDR3.Found.How"] = "a" | |
37 | |
38 out[,added_summary_columns] = summ[,added_summary_columns] | |
39 | |
40 out[,added_sequence_columns] = aa[,added_sequence_columns] | |
41 | |
42 out[,added_junction_columns] = junction[,added_junction_columns] | |
43 | |
44 out[,"Top V Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"])) | |
45 out[,"Top D Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"])) | |
46 out[,"Top J Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"])) | |
47 | |
48 out = out[!grepl("Less than", summ[,"V.GENE.and.allele"]),] | |
49 out = out[!grepl("Less than", summ[,"D.GENE.and.allele"]),] | |
50 out = out[!grepl("Less than", summ[,"J.GENE.and.allele"]),] | |
51 | |
52 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')] | |
53 | |
54 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') | |
55 | |
56 out[,"VDJ Frame"] = as.character(out[,"VDJ Frame"]) | |
57 | |
58 fltr = out[,"VDJ Frame"] == "in-frame" | |
59 if(any(fltr)){ | |
60 out[fltr, "VDJ Frame"] = "In-frame" | |
61 } | |
62 | |
63 fltr = out[,"VDJ Frame"] == "null" | |
64 if(any(fltr)){ | |
65 out[fltr, "VDJ Frame"] = "Out-of-frame" | |
66 } | |
67 | |
68 fltr = out[,"VDJ Frame"] == "out-of-frame" | |
69 if(any(fltr)){ | |
70 out[fltr, "VDJ Frame"] = "Out-of-frame" | |
71 } | |
72 | |
73 fltr = out[,"VDJ Frame"] == "" | |
74 if(any(fltr)){ | |
75 out[fltr, "VDJ Frame"] = "Out-of-frame" | |
76 } | |
77 | |
78 for(col in c('Top V Gene','Top D Gene','Top J Gene')){ | |
79 out[,col] = as.character(out[,col]) | |
80 fltr = out[,col] == "" | |
81 fltr[is.na(fltr)] = T | |
82 if(any(fltr)){ | |
83 out[fltr,col] = "NA" | |
84 } | |
85 } | |
86 | |
87 write.table(out, out.file, sep="\t", quote=F, row.names=F, col.names=T) |