Mercurial > repos > proteore > proteore_prot_features
diff add_protein_features.R @ 18:0a9ae3d7dbf2 draft default tip
"planemo upload commit 7afd4b3ee25f024257ccbac6e51076d25b2a04e7"
author | proteore |
---|---|
date | Thu, 20 Aug 2020 03:09:52 -0400 |
parents | 7caa90759aba |
children |
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--- a/add_protein_features.R Fri Jan 24 05:04:15 2020 -0500 +++ b/add_protein_features.R Thu Aug 20 03:09:52 2020 -0400 @@ -48,9 +48,7 @@ --column: the column number which you would like to apply... --header: true/false if your file contains a header --type: the type of input IDs (Uniprot_AC/EntrezID) - --pc_features: IsoPoint,SeqLength,MW - --localization: Chr,SubcellLocations - --diseases_info: Diseases + --pc_features: IsoPoint,SeqLength,MW,Chr,SubcellLocations,Diseases,protein_name,function,post_trans_mod,protein_family,pathway --output: text output filename \n") q(save="no") @@ -122,14 +120,9 @@ # Get information from neXtProt get_nextprot_info <- function(nextprot,input,pc_features,localization,diseases_info){ - if(diseases_info){ - cols = c("NextprotID",pc_features,localization,"Diseases") - } else { - cols = c("NextprotID",pc_features,localization) - } - + cols = c("NextprotID",pc_features) cols=cols[cols!="None"] - info = nextprot[match(input,nextprot$NextprotID),cols] + info = nextprot[match(input,nextprot$NextprotID),intersect(colnames(nextprot),cols)] return(info) } @@ -172,8 +165,6 @@ # Parse arguments id_type = args$type pc_features = strsplit(args$pc_features, ",")[[1]] - localization = strsplit(args$localization, ",")[[1]] - diseases_info = str2bool(args$diseases_info) output = args$output # Change the sample ids if they are Uniprot_AC ids to be able to match them with @@ -191,7 +182,7 @@ if (all(!NextprotID %in% nextprot[,1])){ write.table("None of the input ids can be found in Nextprot",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE) } else { - res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info) + res <- get_nextprot_info(nextprot,NextprotID,pc_features) res = res[!duplicated(res$NextprotID),] output_content = merge(file, res,by.x=ncol,by.y="NextprotID",incomparables = NA,all.x=T) output_content = order_columns(output_content,ncol,id_type,file)