Mercurial > repos > davidvanzessen > argalaxy_tools
view imgt_loader/imgt_loader.r @ 42:9a47d7a552d6 draft
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author | davidvanzessen |
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date | Thu, 26 Oct 2017 09:08:37 -0400 |
parents | 106275b54470 |
children | 4d2a8f98a502 |
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args <- commandArgs(trailingOnly = TRUE) options(show.error.locations = TRUE) summ.file = args[1] sequences.file = args[2] aa.file = args[3] junction.file = args[4] gapped.aa.file = args[5] out.file = args[6] print(summ.file) print(out.file) summ = read.table(summ.file, sep="\t", header=T, quote="", fill=T) sequences = read.table(sequences.file, sep="\t", header=T, quote="", fill=T) aa = read.table(aa.file, sep="\t", header=T, quote="", fill=T) gapped.aa = read.table(gapped.aa.file, sep="\t", header=T, quote="", fill=T) junction = read.table(junction.file, sep="\t", header=T, quote="", fill=T) print(paste("nrow(summ)", nrow(summ))) write.table(summ, out.file, sep="\t", quote=F, row.names=F, col.names=T) fix_column_names = function(df){ if("V.DOMAIN.Functionality" %in% names(df)){ names(df)[names(df) == "V.DOMAIN.Functionality"] = "Functionality" print("found V.DOMAIN.Functionality, changed") } if("V.DOMAIN.Functionality.comment" %in% names(df)){ names(df)[names(df) == "V.DOMAIN.Functionality.comment"] = "Functionality.comment" print("found V.DOMAIN.Functionality.comment, changed") } return(df) } summ = fix_column_names(summ) sequences = fix_column_names(sequences) aa = fix_column_names(aa) gapped.aa = fix_column_names(gapped.aa) junction = fix_column_names(junction) print(paste("nrow(summ)", nrow(summ))) 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') old_sequence_columns=c('CDR1.IMGT','CDR2.IMGT','CDR3.IMGT') old_junction_columns=c('JUNCTION') added_summary_columns=c('Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence') added_sequence_columns=c('FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT') 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') 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') out=summ[,c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")] print(paste("nrow(summ)", nrow(summ))) print(paste("nrow(aa)", nrow(aa))) out[,"CDR1.Seq"] = aa[,"CDR1.IMGT"] out[,"CDR1.Length"] = summ[,"CDR1.IMGT.length"] out[,"CDR2.Seq"] = aa[,"CDR2.IMGT"] out[,"CDR2.Length"] = summ[,"CDR2.IMGT.length"] out[,"CDR3.Seq"] = gapped.aa[,"CDR3.IMGT"] out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"] out[,"CDR3.IMGT"] = out[,"CDR3.Seq"] out[,"CDR3.Seq.DNA"] = sequences[,"CDR3.IMGT"] out[,"CDR3.Length.DNA"] = nchar(as.character(out[,"CDR3.Seq.DNA"])) out[,"Strand"] = summ[,"Orientation"] out[,"CDR3.Found.How"] = "a" out[,added_summary_columns] = summ[,added_summary_columns] out[,added_sequence_columns] = aa[,added_sequence_columns] out[,added_junction_columns] = junction[,added_junction_columns] out[,"Top V Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"])) out[,"Top D Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"])) out[,"Top J Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"])) out = out[!grepl("Less than", summ[,"V.GENE.and.allele"]),] out = out[!grepl("Less than", summ[,"D.GENE.and.allele"]),] out = out[!grepl("Less than", summ[,"J.GENE.and.allele"]),] 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')] 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') out[,"VDJ Frame"] = as.character(out[,"VDJ Frame"]) fltr = out[,"VDJ Frame"] == "in-frame" if(any(fltr, na.rm=T)){ out[fltr, "VDJ Frame"] = "In-frame" } fltr = out[,"VDJ Frame"] == "null" if(any(fltr, na.rm = T)){ out[fltr, "VDJ Frame"] = "Out-of-frame" } fltr = out[,"VDJ Frame"] == "out-of-frame" if(any(fltr, na.rm = T)){ out[fltr, "VDJ Frame"] = "Out-of-frame" } fltr = out[,"VDJ Frame"] == "" if(any(fltr, na.rm = T)){ out[fltr, "VDJ Frame"] = "Out-of-frame" } for(col in c('Top V Gene','Top D Gene','Top J Gene')){ out[,col] = as.character(out[,col]) fltr = out[,col] == "" fltr[is.na(fltr)] = T if(any(fltr, na.rm = T)){ out[fltr,col] = "NA" } } write.table(out, out.file, sep="\t", quote=F, row.names=F, col.names=T)