| Previous changeset 14:659f1248f535 (2018-09-19) Next changeset 16:b6607b7e683f (2019-01-28) |
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Commit message:
planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b |
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modified:
README.rst id_converter.xml tool_data_table_conf.xml.sample |
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added:
id_converter.R tool-data/human_id_mapping_23-10-2018.tsv tool-data/mouse_id_mapping_23-10-2018.tsv tool-data/proteore_id_mapping.loc.sample tool-data/rat_id_mapping_23-10-2018.tsv |
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removed:
id_converter_UniProt.R tool-data/human_id_mapping_file.tsv tool-data/id_mapping.loc.sample tool-data/mouse_id_mapping.tsv |
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| diff -r 659f1248f535 -r b50d913ec067 README.rst --- a/README.rst Wed Sep 19 04:45:04 2018 -0400 +++ b/README.rst Tue Dec 18 09:57:21 2018 -0500 |
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| @@ -3,7 +3,7 @@ **Authors** -T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform @@ -51,10 +51,35 @@ * Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930) +* BioGrid (e.g. 113361) + +* STRING (e.g. 9606.ENSP00000300161) + +* KEGG gene id (e.g. hsa:7529) + +.. class:: warningmark + +Nextprot and OMIM are only available for Human. + This tool converts human IDs using file built from: -* HUMAN_9606_idmapping_selected.tab +* HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018) + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ + +* HUMAN_9606_idmapping.dat (Uniprot 23/10/18) Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ -* nextprot_ac_list_all.txt - Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ \ No newline at end of file +* nextprot_ac_list_all.txt (Nextprot released on 10/10/2018) + Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ + +* MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018) + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ + +* MOUSE_10090_idmapping.dat (Uniprot 23/10/18) + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ + +* RAT_10116_idmapping.dat (Uniprot 23/10/18) + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ + +* RAT_10116_idmapping_selected.tab (Uniprot 23/10/18) + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ |
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| diff -r 659f1248f535 -r b50d913ec067 id_converter.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/id_converter.R Tue Dec 18 09:57:21 2018 -0500 |
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| @@ -0,0 +1,185 @@ +# Read file and return file content as data.frame +read_file <- function(path,header){ + file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"",check.names = F),silent=TRUE) + if (inherits(file,"try-error")){ + stop("File not found !") + }else{ + return(file) + } +} + +str2bool <- function(x){ + if (any(is.element(c("t","true"),tolower(x)))){ + return (TRUE) + }else if (any(is.element(c("f","false"),tolower(x)))){ + return (FALSE) + }else{ + return(NULL) + } +} + +mapping_ids <- function(list_id,input_id_type,ref_file,options){ + list_id = list_id[!is.na(list_id)] + if (!any(grep(";",ref_file[input_id_type]))) { + res <- ref_file[match(list_id,ref_file[input_id_type][,]),c(input_id_type,options)] + res=as.data.frame(res) + res=res[which(!is.na(res[,1])),] + row.names(res)=res[,1] + res=res[2:ncol(res)] + } else { + if (length(options) > 1) { + res <- data.frame(t(sapply(list_id, function(x) apply(ref_file[grep(x,ref_file[input_id_type][,]),options],2,function(y) paste(y[y!=""],sep="",collapse=";")) ))) + } else if (length(options)==1){ + res <- data.frame(sapply(list_id, function(x) gsub(";+$","",paste(ref_file[grep(x,ref_file[input_id_type][,]),options],sep="",collapse=";")))) + colnames(res)=options + } + } + + return (res) +} + +get_list_from_cp <-function(list){ + list = strsplit(list, "[ \t\n]+")[[1]] + list = list[list != ""] #remove empty entry + list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2") + return(list) +} + +order_columns <- function (df,ncol){ + if (ncol==1){ #already at the right position + return (df) + } else { + df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])] + } + return (df) +} + +#take data frame, return data frame +split_ids_per_line <- function(line,ncol){ + + #print (line) + header = colnames(line) + line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol]) + + if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) { + if (length(line)==1 ) { + lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F) + } else { + if (ncol==1) { #first column + lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)])) + } else if (ncol==length(line)) { #last column + lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";")))) + } else { + lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)])) + } + } + colnames(lines)=header + return(lines) + } else { + return(line) + } +} + +#create new lines if there's more than one id per cell in the columns in order to have only one id per line +one_id_one_line <-function(tab,ncol){ + + if (ncol(tab)>1){ + + tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x)) + header=colnames(tab) + res=as.data.frame(matrix(ncol=ncol(tab),nrow=0)) + for (i in 1:nrow(tab) ) { + lines = split_ids_per_line(tab[i,],ncol) + res = rbind(res,lines) + } + }else { + res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F) + res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F) + colnames(res)=colnames(tab) + } + return(res) +} + +get_args <- function(){ + args <- commandArgs(TRUE) + if(length(args)<1) { + args <- c("--help") + } + + # Help section + if("--help" %in% args) { + cat("Selection and Annotation HPA + Arguments: + --ref_file: path to reference file (id_mapping_file.txt) + --input_type: type of input (list of id or filename) + --id_type: type of input IDs + --input: list of IDs (text or filename) + --column_number: the column number which contains list of input IDs + --header: true/false if your file contains a header + --target_ids: target IDs to map to + --output: output filename \n") + q(save="no") + } + + # Parse arguments + parseArgs <- function(x) strsplit(sub("^--", "", x), "=") + argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) + args <- as.list(as.character(argsDF$V2)) + names(args) <- argsDF$V1 + + return(args) +} + +mapping = function() { + + args <- get_args() + + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/id_converter/args.rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/id_converter/args.rda") + + input_id_type = args$id_type # Uniprot, ENSG.... + list_id_input_type = args$input_type # list or file + options = strsplit(args$target_ids, ",")[[1]] + output = args$output + id_mapping_file = args$ref_file + + # Extract input IDs + if (list_id_input_type == "list") { + list_id = get_list_from_cp(args$input) + } else if (list_id_input_type == "file") { + filename = args$input + column_number = as.numeric(gsub("c", "" ,args$column_number)) + header = str2bool(args$header) + file_all = read_file(filename, header) + file_all = one_id_one_line(file_all,column_number) + list_id = trimws(gsub("[$,\xc2\xa0]","",sapply(strsplit(as.character(file_all[,column_number]), ";"), "[", 1))) + # Remove isoform accession number (e.g. "-2") + list_id = unique(gsub("-.+", "", list_id)) + } + + # Extract ID maps + id_map = read_file(id_mapping_file, T) + + # Map IDs + res <- mapping_ids(list_id,input_id_type,id_map,options) + + #merge data frames + if (list_id_input_type == "list"){ + list_id <- data.frame(list_id) + output_content = merge(list_id,res,by.x=1,by.y="row.names",incomparables = NA, all.x=T) + colnames(output_content)[1]=input_id_type + } else if (list_id_input_type == "file") { + output_content = merge(file_all,res,by.x=column_number,by.y="row.names",incomparables = NA, all.x=T) + output_content = order_columns(output_content,column_number) + } + + #write output + header=colnames(output_content) + output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) + colnames(output_content)=header + write.table(output_content, output, row.names = FALSE, sep = '\t', quote = FALSE) +} + +mapping() + +#Rscript id_converter_UniProt.R "UniProt.AC" "test-data/UnipIDs.txt,c1,false" "file" "Ensembl_PRO,Ensembl,neXtProt_ID" "test-data/output.txt" ../../utils/mapping_file.txt |
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| diff -r 659f1248f535 -r b50d913ec067 id_converter.xml --- a/id_converter.xml Wed Sep 19 04:45:04 2018 -0400 +++ b/id_converter.xml Tue Dec 18 09:57:21 2018 -0500 |
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| b'@@ -1,5 +1,5 @@\n-<tool id="IDconverter" name="ID Converter" version="2018.09.18">\n- <description>convert public database identifiers\n+<tool id="IDconverter" name="ID Converter" version="2018.12.18">\n+ <description>(Human, Mouse, Rat)\n </description>\n <requirements>\n <requirement type="package" version="3.4.1">R</requirement>\n@@ -8,7 +8,7 @@\n <exit_code range="1:" />\n </stdio>\n <command interpreter="Rscript">\n- $__tool_directory__/id_converter_UniProt.R\n+ $__tool_directory__/id_converter.R\n --id_type="$species.idtypein"\n #if $input.ids == "text"\n --input="$input.txt"\n@@ -21,17 +21,17 @@\n #end if\n --target_ids="$species.idto.idtypeout"\n --output="$output"\n- --ref_file="$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.mapping_file ), $__app__.tool_data_tables[\'id_mapping_tab\'].get_fields() )[0][-1] }"\n+ --ref_file="$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.mapping_file ), $__app__.tool_data_tables[\'proteore_id_mapping\'].get_fields() )[0][-1] }"\n \n </command>\n <inputs>\n <conditional name="input" >\n- <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >\n+ <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" >\n <option value="text">Copy/paste your identifiers</option>\n- <option value="file" selected="true">Input file containing your identifiers</option>\n+ <option value="file" selected="true">Input file containing IDs</option>\n </param>\n <when value="text" >\n- <param name="txt" type="text" label="Copy/paste your identifiers" help=\'IDs must be separated by "," into the form field, for example: P31946,P62258\' >\n+ <param name="txt" type="text" label="Copy/paste IDs" help=\'IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258\' >\n <sanitizer invalid_char="">\n <valid initial="string.printable">\n <remove value="'"/>\n@@ -47,27 +47,28 @@\n </param>\n </when>\n <when value="file" >\n- <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />\n- <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />\n- <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help=\'For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on\' /> \n+ <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />\n+ <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />\n+ <param name="ncol" type="text" value="c1" label="Column number of IDs to map" help=\'For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on\' /> \n </when>\n </conditional>\n <conditional name="species">\n- <param name="mapping_file" type="select" label="Select species for ID conversion" >\n- <options from_data_table="id_mapping_tab"/>\n+ <param name="mapping_file" type="select" label="Species" >\n+ <options from_data_table="proteore_id_mapping"/>\n <option value="human_id_mapping"></option>\n <option value="mouse_id_mapping"></option>\n+ <option value="rat_id_mapping"></option>\n </param>\n <when value="human_id_mapping">\n- <param name'..b'olumn file, the mapped IDs column(s) will be added at the end of the input file.\n \n-**Available databases**\n+.. class:: warningmark\n+\n+Accession numbers with an hyphen ("-") that normally correspond to isoform are considered as similar to its canonical form.\n+For example, "Q71U36-2" will be treated as "Q71U36".\n+\n+-----\n+\n+**Parameters**\n+Target type of IDs currently supported: \n \n * neXtProt ID (e.g. NX_P31946)\n \n-* Uniprot accession number (e.g. P31946)\n+* UniProt accession number (e.g. P31946)\n \n-* Uniprot ID (e.g 1433B_HUMAN)\n+* UniProt ID (e.g 1433B_HUMAN)\n \n * Entrez gene ID (e.g. 7529)\n \n-* RefSeq (NCBI) protein (e.g. NP_003395.1)\n+* RefSeq protein (NCBI) (e.g. NP_003395.1)\n \n-* GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)\n+* GI (NCBI GI number) (e.g. 21328448)\n \n * Protein DataBank ID (e.g. 2BR9:A)\n \n@@ -202,29 +252,36 @@\n \n * Ensembl protein ID (e.g. ENSP00000300161)\n \n+* BioGrid (e.g. 113361)\n+\n+* STRING (e.g. 9606.ENSP00000300161)\n+\n+* KEGG gene id (e.g. hsa:7529)\n+\n+.. class:: warningmark \n+\n+Nextprot and OMIM only applicable to Human species.\n+\n -----\n \n-.. class:: infomark\n+**Output**\n+\n+A text file containing the selected type of IDs (in addition to the original column(s) provided)\n+Please, note that a "NA" is returned when there is no match between a source ID and the corresponding target ID.\n+\n+-----\n+\n+**Data sources (release date)**\n \n This tool converts human IDs using the following source files:\n \n-* HUMAN_9606_idmapping_selected.tab (Uniprot 02/07/2018)\n- Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n-\n-* HUMAN_9606_idmapping.dat (Uniprot 02/07/18)\n- Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n-\n-* nextprot_ac_list_all.txt (Nextprot released on 17/01/2018)\n- Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/\n-\n------\n-\n-.. class:: warningmark\n-\n-Accession numbers with an hyphen ("-") that normally correspond to isoform are considered \n-(and will therefore be treated) as similar to its canonical form.\n-\n-For example, "Q71U36-2" will be treated as "Q71U36".\n+- **HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n+- **HUMAN_9606_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n+- **nextprot_ac_list_all.txt (Nextprot released on 10/10/2018)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/\n+- **MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n+- **MOUSE_10090_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n+- **RAT_10116_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n+- **RAT_10116_idmapping_selected.tab (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/\n \n -----\n \n@@ -232,9 +289,9 @@\n \n **Authors**\n \n-T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR\n+David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR\n \n-Sandra D\xc3\xa9rozier, Olivier Ru\xc3\xa9, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform\n+Sandra D\xc3\xa9rozier, Olivier Ru\xc3\xa9, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR\n \n This work has been partially funded through the French National Agency for Research (ANR) IFB project.\n \n' |
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| diff -r 659f1248f535 -r b50d913ec067 id_converter_UniProt.R --- a/id_converter_UniProt.R Wed Sep 19 04:45:04 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,126 +0,0 @@ -# Read file and return file content as data.frame -readfile = function(filename, header) { - if (header == "true") { - # Read only first line of the file as header: - headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") - #Read the data of the files (skipping the first row) - file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") - # Remove empty rows - file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] - #And assign the header to the data - names(file) <- headers - } - else { - file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") - # Remove empty rows - file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] - } - return(file) -} - -# Mapping IDs using file built from -# - HUMAN_9606_idmapping_selected.tab -# Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ -# - nextprot_ac_list_all.txt -# Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ -# Available databases: -# UNIPROT_AC: Uniprot accession number (e.g. P31946) -# UNIPROT_ID: Uniprot identifiers (e.g 1433B_HUMAN) -# GeneID_EntrezGene: Entrez gene ID (serie of digit) (e.g. 7529) -# RefSeq: RefSeq (NCBI) protein (e.g. NP_003395.1; NP_647539.1; XP_016883528.1) -# GI_number: GI (NCBI GI number) ID (serie of digits) assigned to each sequence record processed by NCBI (e.g; 21328448; 377656701; 67464627; 78101741) -# PDB: Protein DataBank Identifiers (e.g. 2BR9:A; 3UAL:A; 3UBW:A) -# GO_ID: GOterms (Gene Ontology) Identifiers (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634) -# PIR: Protein Information Resource ID (e.g. S34755) -# OMIM: OMIM (Online Mendelian Inheritance in Man database) ID (serie of digits) (e.g: 601289) -# UniGene: Unigene Identifier (e.g. Hs.643544) -# Ensembl_ENSG: Ensembl gene identifiers (e.g. ENSG00000166913) -# Ensembl_ENST: Ensembl transcript identifiers (e.g. ENST00000353703; ENST00000372839) -# Ensembl_ENSP: Ensembl protein identifiers (e.g. ENSP00000300161; ENSP00000361930) - -mapping = function() { - args <- commandArgs(TRUE) - if(length(args)<1) { - args <- c("--help") - } - - # Help section - if("--help" %in% args) { - cat("Selection and Annotation HPA - Arguments: - --ref_file: path to reference file (id_mapping_file.txt) - --input_type: type of input (list of id or filename) - --id_type: type of input IDs - --input: list of IDs (text or filename) - --column_number: the column number which contains list of input IDs - --header: true/false if your file contains a header - --target_ids: target IDs to map to - --output: output filename \n") - q(save="no") - } - - # Parse arguments - parseArgs <- function(x) strsplit(sub("^--", "", x), "=") - argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) - args <- as.list(as.character(argsDF$V2)) - names(args) <- argsDF$V1 - - input_id_type = args$id_type # Uniprot, ENSG.... - list_id_input_type = args$input_type # list or file - options = strsplit(args$target_ids, ",")[[1]] - output = args$output - id_mapping_file = args$ref_file - - # Extract input IDs - if (list_id_input_type == "list") { - print(args$input) - list_id = trimws(strsplit(args$input, ",")[[1]]) - list_id = list_id[list_id != ""] #remove empty entry - # Remove isoform accession number (e.g. "-2") - list_id = gsub("-.+", "", list_id) - } else if (list_id_input_type == "file") { - filename = args$input - column_number = as.numeric(gsub("c", "" ,args$column_number)) - header = args$header - file_all = readfile(filename, header) - list_id = trimws(gsub("[$,\xc2\xa0]","",sapply(strsplit(file_all[,column_number], ";"), "[", 1))) - # Remove isoform accession number (e.g. "-2") - list_id = gsub("-.+", "", list_id) - } - - # Extract ID maps - id_map = read.table(id_mapping_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "") - - names = c() - - # Map IDs - res = matrix(nrow=length(list_id), ncol=0) - - for (opt in options) { - names = c(names, opt) - mapped = id_map[match(list_id, id_map[input_id_type][,]),][opt][,] - res = cbind(res, matrix(mapped)) - } - - # Write output - if (list_id_input_type == "list") { - res = cbind(as.matrix(list_id), res) - names = c(input_id_type, names) - colnames(res) = names - write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE) - } - else if (list_id_input_type == "file") { - names(res) = options - if (all(names(file_all) == file_all[1,1:length(names(file_all))])){ #if header of file is the same as the first line of file - names(file_all)[column_number] = input_id_type - } - names = c(names(file_all), names) - output_content = cbind(file_all, res) - colnames(output_content) = names - write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE) - } -} - -mapping() - -#Rscript id_converter_UniProt.R "UniProt.AC" "test-data/UnipIDs.txt,c1,false" "file" "Ensembl_PRO,Ensembl,neXtProt_ID" "test-data/output.txt" ../../utils/mapping_file.txt |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool-data/human_id_mapping_23-10-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/human_id_mapping_23-10-2018.tsv Tue Dec 18 09:57:21 2018 -0500 |
| b |
| b'@@ -0,0 +1,174356 @@\n+UniProt-AC\tUniProt-ID\tGeneID\tRefSeq\tGI\tPDB\tGO\tPIR\tMIM\tUniGene\tEnsembl_Gene\tEnsembl_Transcript\tEnsembl_Protein\tneXtProt\tBioGrid\tSTRING\tKEGG\r\n+P31946\t1433B_HUMAN\t7529\tNP_003395.1; NP_647539.1; XP_016883528.1\t4507949; 377656702; 67464628; 1345590; 1034625756; 21328448; 377656701; 67464627; 78101741\t2BQ0:A; 2BQ0:B; 2C23:A; 4DNK:A; 4DNK:B; 5N10:A; 5N10:B; 6BYK:A; 6BYK:B; 6BYK:C; 6BYK:D\tGO:0005737; GO:0005829; GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634; GO:0048471; GO:0017053; GO:0045296; GO:0019899; GO:0042826; GO:0042802; GO:0051219; GO:0050815; GO:0008022; GO:0019904; GO:0044877; GO:0051220; GO:0035329; GO:0000165; GO:0061024; GO:0045744; GO:0035308; GO:0045892; GO:0043085; GO:1900740; GO:0051291; GO:0006605; GO:0043488; GO:0016032\tS34755\t601289\tHs.643544\tENSG00000166913\tENST00000353703; ENST00000372839\tENSP00000300161; ENSP00000361930\tNX_P31946\t113361\t9606.ENSP00000300161\thsa:7529\r\n+P62258\t1433E_HUMAN\t7531\tNP_006752.1\t374074368; 62131678; 67464424; 194379794; 221045758; 5803225; 374074366; 51702210\t2BR9:A; 3UAL:A; 3UBW:A; 6EIH:A\tGO:0090724; GO:0005737; GO:0005829; GO:0070062; GO:0005925; GO:0098978; GO:0005871; GO:0042470; GO:0016020; GO:0005739; GO:0005634; GO:0045296; GO:0005246; GO:0019899; GO:0042826; GO:0042802; GO:0044325; GO:0023026; GO:0051219; GO:0050815; GO:0015459; GO:0019904; GO:0046982; GO:0017112; GO:0003723; GO:0097110; GO:0031625; GO:0034605; GO:0021987; GO:0097711; GO:0000086; GO:0035329; GO:0021766; GO:0035556; GO:0000165; GO:0061024; GO:0086013; GO:1905913; GO:1901020; GO:0043154; GO:1902309; GO:0001764; GO:0046827; GO:1900740; GO:0034504; GO:0006605; GO:1900034; GO:0051480; GO:0010389; GO:0086091; GO:0003064; GO:0060306; GO:0099072; GO:1901016; GO:0021762; GO:0016032\tA61235; I38947\t605066\tHs.513851\tENSG00000108953; ENSG00000274474\tENST00000264335; ENST00000571732; ENST00000616643; ENST00000627231\tENSP00000264335; ENSP00000461762; ENSP00000481059; ENSP00000487356\tNX_P62258\t113363\t9606.ENSP00000264335\thsa:7531\r\n+Q04917\t1433F_HUMAN\t7533\tNP_003396.1\t4507951; 437363; 83754686; 83754699; 83754700; 1345593; 83754684; 83754685; 28862; 83754683\t2C63:A; 2C63:B; 2C63:C; 2C63:D; 2C74:A; 2C74:B\tGO:0005737; GO:0005829; GO:0070062; GO:0098978; GO:0014704; GO:0005739; GO:0005886; GO:0098793; GO:0003779; GO:0019899; GO:0035259; GO:0042802; GO:0005159; GO:0044325; GO:0019904; GO:0046982; GO:0017080; GO:0006713; GO:0042921; GO:0006886; GO:0086010; GO:0061024; GO:0050774; GO:1900740; GO:0045893; GO:0045664; GO:2000649; GO:0002028; GO:0048167; GO:0021762\tS34756; S38509; S38532\t113508\tHs.226755\tENSG00000128245\tENST00000248975\tENSP00000248975\tNX_Q04917\t113365\t9606.ENSP00000248975\thsa:7533\r\n+P61981\t1433G_HUMAN\t7532\tNP_036611.2\t6016838; 380764684; 635576381; 82407956; 82407958; 550545213; 635576377; 380765197; 82407950; 550545214; 119592210; 1006588564; 1006588561; 635576379; 21464101; 82407952; 48428721; 5726310; 550545212; 635576378; 1006588559; 18088513; 49456805; 1006588565; 550545215; 1006588558; 49456763; 1006588562; 82407948; 82407954; 635576376; 635576380\t2B05:A; 2B05:B; 2B05:C; 2B05:D; 2B05:E; 2B05:F; 3UZD:A; 4E2E:A; 4J6S:A; 4J6S:B; 4J6S:C; 4J6S:D; 4O46:A; 4O46:B; 4O46:C; 4O46:D; 4O46:E; 4O46:F; 5D3E:A; 5D3E:B; 5D3E:E; 5D3E:F; 5D3E:I; 5D3E:J; 6BYJ:A; 6BYJ:B; 6BYJ:C; 6BYJ:D; 6BYJ:E; 6BYJ:F; 6BYL:A; 6BYL:B; 6BYL:C; 6BYL:D; 6BYL:E; 6BYL:F; 6BZD:A; 6BZD:B; 6BZD:C; 6BZD:D; 6FEL:A; 6FEL:B; 6FEL:C; 6FEL:D\tGO:0005829; GO:0070062; GO:0005925; GO:0016020; GO:0005739; GO:0043209; GO:0098793; GO:0042802; GO:0005159; GO:0019904; GO:0005080; GO:0008426; GO:0030971; GO:0003723; GO:0032869; GO:0097711; GO:0000086; GO:0061024; GO:0006469; GO:1900740; GO:0006605; GO:0010389; GO:0045664; GO:0009966; GO:0048167\t\t605356; 617665\tHs.744840\tENSG00000170027\tENST00000307630\tENSP00000306330\tNX_P61981\t113364\t9606.ENSP00000306330\thsa:7532\r\n+P31947\t1433S_HUMAN\t2810\tNP_006133.1\t436408756; 306991738; 969812714; 350610438; 350610440; 2702355; 393715161; 394985958; 398953; 305677674; 305677670; 350610436; 52'..b'218\t\t\t\t\t\t\t\r\n+E0ZMB5\tE0ZMB5_HUMAN\t\t\t305671495\t\tGO:0016020; GO:0016758; GO:0005975\t\t\tHs.654423\t\t\t\t\t\t\t\r\n+G3V5R6\tG3V5R6_HUMAN\t\t\t\t\t\t\t\t\tENSG00000151338\tENST00000555870\tENSP00000452478\t\t\t\t\r\n+G3V5W2\tG3V5W2_HUMAN\t\t\t\t\tGO:0016021; GO:0022857\t\t\t\tENSG00000155465\tENST00000555911\tENSP00000452551\t\t\t\t\r\n+H0Y594\tH0Y594_HUMAN\t\t\t\t\t\t\t\t\tENSG00000125676\tENST00000448128\tENSP00000397317\t\t\t\t\r\n+H0YIC4\tH0YIC4_HUMAN\t\t\t\t\tGO:0016021; GO:0046912; GO:0006099\t\t\t\tENSG00000062485\tENST00000548746\tENSP00000449080\t\t\t\t\r\n+H2B3F1\tH2B3F1_HUMAN\t\t\t373809834\t\tGO:0016021; GO:0042612; GO:0002474; GO:0006955\t\t\tHs.656020; Hs.743218\t\t\t\t\t\t\t\r\n+Q5HYC7\tQ5HYC7_HUMAN\t\t\t57997566\t\tGO:0005887; GO:0015379; GO:0071477\t\t\tHs.510939\t\t\t\t\t\t\t\r\n+Q8N811\tQ8N811_HUMAN\t\t\t21757234\t\t\t\t\t\t\t\t\t\t\t\t\r\n+Q92646\tQ92646_HUMAN\t\t\t1568545\t\tGO:0000786; GO:0005634; GO:0003677; GO:0046982\t\t\t\t\t\t\t\t\t\t\r\n+Q9HAD7\tQ9HAD7_HUMAN\t\t\t40033469; 10433122\t\tGO:0016021\t\t\tHs.124673\t\t\t\t\t\t\t\r\n+Q9HAH9\tQ9HAH9_HUMAN\t\t\t10432890; 40033302\t\t\t\t\tHs.511265\t\t\t\t\t\t\t\r\n+C5IZY2\tC5IZY2_HUMAN\t\t\t239812658\t\t\t\t\tHs.656020; Hs.743218\t\t\t\t\t\t\t\r\n+H0Y5B5\tH0Y5B5_HUMAN\t\t\t\t\tGO:0016586; GO:0003682; GO:0006338\t\t\t\tENSG00000163939\tENST00000446103\tENSP00000397662\t\t\t\t\r\n+H0Y5M0\tH0Y5M0_HUMAN\t\t\t\t\t\t\t\t\tENSG00000151948\tENST00000413816\tENSP00000399374\t\t\t\t\r\n+H0YBD9\tH0YBD9_HUMAN\t\t\t\t\t\t\t\t\tENSG00000176623\tENST00000517710\tENSP00000429287\t\t\t\t\r\n+H0YC08\tH0YC08_HUMAN\t\t\t\t\t\t\t\t\tENSG00000170234\tENST00000520662\tENSP00000430703\t\t\t\t\r\n+H0YC55\tH0YC55_HUMAN\t\t\t\t\tGO:0030261\t\t\t\tENSG00000025770\tENST00000522304\tENSP00000430944\t\t\t\t\r\n+H0YHK5\tH0YHK5_HUMAN\t\t\t\t\t\t\t\t\tENSG00000186710\tENST00000550918\tENSP00000447276\t\t\t\t\r\n+H2AM04\tH2AM04_HUMAN\t\t\t371784072\t\tGO:0042613; GO:0019882; GO:0006955\t\t\tHs.534322; Hs.696211; Hs.736560\t\t\t\t\t\t\t\r\n+H2BDR3\tH2BDR3_HUMAN\t\t\t341834808\t\t\t\t\tHs.656020; Hs.743218\t\t\t\t\t\t\t\r\n+A0A0A0MTI5\tA0A0A0MTI5_HUMAN\t\t\t\t\tGO:0000062\t\t\t\tENSG00000155368\tENST00000542275\tENSP00000440698\t\t\t\t\r\n+B2RB23\tB2RB23_HUMAN\t\t\t189069404\t\tGO:0016747; GO:0008152\t\t\tHs.200136\t\t\t\t\t\t\t\r\n+B4DDU0\tB4DDU0_HUMAN\t\t\t194373511\t\tGO:0005096; GO:0007165\t\t\tHs.497575; Hs.729527; Hs.744555\t\t\t\t\t\t\t\r\n+B4DJR3\tB4DJR3_HUMAN\t\t\t194382340\t\tGO:0004540; GO:0008033\t\t\tHs.139120\t\t\t\t\t\t\t\r\n+C9J4K2\tC9J4K2_HUMAN\t\t\t\t\tGO:0007015\t\t\t\tENSG00000154556\tENST00000457247\tENSP00000398335\t\t\t\t\r\n+E5RFS6\tE5RFS6_HUMAN\t\t\t\t\t\t\t\t\tENSG00000164620\tENST00000518856\tENSP00000427992\t\t\t\t\r\n+F5GX38\tF5GX38_HUMAN\t\t\t\t\t\t\t\t\tENSG00000133103\tENST00000543804\tENSP00000440473\t\t\t\t\r\n+F5H386\tF5H386_HUMAN\t\t\t\t\tGO:0020037; GO:0036393; GO:0042742; GO:0006979\t\t\t\tENSG00000167419\tENST00000543544\tENSP00000445344\t\t\t\t\r\n+F5H3M2\tF5H3M2_HUMAN\t3801\tNP_001305641.1\t973353100\t\tGO:0005874; GO:0005524; GO:0008569; GO:0008017; GO:0007018\t\t\tHs.23131\tENSG00000140859\tENST00000540079\tENSP00000438805\t\t\t\t\r\n+Q4R1L3\tQ4R1L3_HUMAN\t\t\t67845854\t\tGO:0016021; GO:0005739; GO:0022900\t\t\t\t\t\t\t\t\t\t\r\n+A0A0A0MT90\tA0A0A0MT90_HUMAN\t7697\tNP_001153655.1\t237512951\t\tGO:0005622; GO:0003676; GO:0006355\t\t\tHs.184080\tENSG00000197008\tENST00000494380\tENSP00000419197\t\t\t\t\r\n+A0A0A6YYJ9\tA0A0A6YYJ9_HUMAN\t\t\t32402659; 41387888\t\tGO:0005887; GO:0015125; GO:0015347; GO:0043252\t\t\t\tENSG00000257046\tENST00000540229\tENSP00000441269\t\t\t9606.ENSP00000441269\t\r\n+E9K900\tE9K900_HUMAN\t\t\t290544425\t\tGO:0016021; GO:0005743; GO:0070469; GO:0008137; GO:0042773\t\t\t\t\t\t\t\t\t\t\r\n+E9LWA6\tE9LWA6_HUMAN\t\t\t320117867\t\t\t\t\t\t\t\t\t\t\t\t\r\n+F1D8N1\tF1D8N1_HUMAN\t10062\tNP_005684.2; XP_005252762.1; XP_005252763.1; XP_005252764.1; XP_006718175.1; XP_006718176.1; XP_011518107.1\t578820247; 158254660; 530394897; 194294517; 578820249; 530394895; 530394893; 767965184; 325495449; 119588355\t\tGO:0005634; GO:0003700; GO:0043565; GO:0003707; GO:0008270; GO:0006351\t\t\tHs.438863\t\t\t\t\t\t\thsa:10062\r\n+F5GWE9\tF5GWE9_HUMAN\t\t\t\t\tGO:0016020; GO:0005525; GO:0003924; GO:0007165\t\t\t\tENSG00000134533\tENST00000537647\tENSP00000441860\t\t\t\t\r\n+F5GXT5\tF5GXT5_HUMAN\t\t\t\t\tGO:0005622; GO:0008536; GO:0006886\t\t\t\tENSG00000133704\tENST00000535989\tENSP00000440979\t\t\t\t\r\n+F5H0R6\tF5H0R6_HUMAN\t\t\t\t\t\t\t\t\tENSG00000021300\tENST00000539157\tENSP00000445990\t\t\t\t\r\n+F5H422\tF5H422_HUMAN\t\t\t\t\tGO:0034993; GO:0051015; GO:0090286\t\t\t\tENSG00000131018\tENST00000495090\tENSP00000438508\t\t\t\t\r\n' |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool-data/human_id_mapping_file.tsv --- a/tool-data/human_id_mapping_file.tsv Wed Sep 19 04:45:04 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,174239 +0,0 @@\n-UniProt-AC\tUniProt-ID\tGeneID\tRefSeq\tGI\tPDB\tGO\tPIR\tMIM\tUniGene\tEnsembl_Gene\tEnsembl_Transcript\tEnsembl_Protein\tneXtProt\tBioGrid\tSTRING\tKEGG\r\n-P31946\t1433B_HUMAN\t7529\tNP_003395.1; NP_647539.1; XP_016883528.1\t4507949; 377656702; 67464628; 1345590; 1034625756; 21328448; 377656701; 67464627; 78101741\t2BQ0:A; 2BQ0:B; 2C23:A; 4DNK:A; 4DNK:B; 5N10:A; 5N10:B; 6BYK:A; 6BYK:B; 6BYK:C; 6BYK:D\tGO:0005737; GO:0005829; GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634; GO:0048471; GO:0017053; GO:0045296; GO:0019899; GO:0042826; GO:0042802; GO:0051219; GO:0050815; GO:0008022; GO:0019904; GO:0044877; GO:0003714; GO:0051220; GO:0035329; GO:0000165; GO:0061024; GO:0045744; GO:0035308; GO:0045892; GO:0043085; GO:1900740; GO:0051291; GO:0006605; GO:0043488; GO:0016032\tS34755\t601289\tHs.643544\tENSG00000166913\tENST00000353703; ENST00000372839\tENSP00000300161; ENSP00000361930\tNX_P31946\t113361\t9606.ENSP00000300161\thsa:7529\r\n-P62258\t1433E_HUMAN\t7531\tNP_006752.1\t374074368; 62131678; 67464424; 194379794; 221045758; 5803225; 374074366; 51702210\t2BR9:A; 3UAL:A; 3UBW:A; 6EIH:A\tGO:0090724; GO:0005737; GO:0005829; GO:0070062; GO:0005925; GO:0005871; GO:0042470; GO:0016020; GO:0005739; GO:0005634; GO:0045296; GO:0005246; GO:0019899; GO:0042826; GO:0042802; GO:0044325; GO:0023026; GO:0051219; GO:0050815; GO:0015459; GO:0019904; GO:0046982; GO:0017112; GO:0003723; GO:0097110; GO:0031625; GO:0034605; GO:0021987; GO:0097711; GO:0000086; GO:0035329; GO:0021766; GO:0035556; GO:0000165; GO:0061024; GO:0086013; GO:1905913; GO:1901020; GO:0043154; GO:1902309; GO:0001764; GO:0046827; GO:1900740; GO:0034504; GO:0006605; GO:1900034; GO:0051480; GO:0010389; GO:0086091; GO:0003064; GO:0060306; GO:1901016; GO:0021762; GO:0016032\tA61235; I38947\t605066\tHs.513851\tENSG00000108953; ENSG00000274474\tENST00000264335; ENST00000571732; ENST00000616643; ENST00000627231\tENSP00000264335; ENSP00000461762; ENSP00000481059; ENSP00000487356\tNX_P62258\t113363\t9606.ENSP00000264335\thsa:7531\r\n-Q04917\t1433F_HUMAN\t7533\tNP_003396.1\t4507951; 437363; 83754686; 83754699; 83754700; 1345593; 83754684; 83754685; 28862; 83754683\t2C63:A; 2C63:B; 2C63:C; 2C63:D; 2C74:A; 2C74:B\tGO:0005737; GO:0005829; GO:0070062; GO:0014704; GO:0005739; GO:0005886; GO:0003779; GO:0019899; GO:0035259; GO:0042802; GO:0005159; GO:0044325; GO:0019904; GO:0046982; GO:0017080; GO:0006713; GO:0042921; GO:0006886; GO:0086010; GO:0061024; GO:0050774; GO:1900740; GO:0045893; GO:0045664; GO:2000649; GO:0002028; GO:0048167; GO:0021762\tS34756; S38509; S38532\t113508\tHs.226755\tENSG00000128245\tENST00000248975\tENSP00000248975\tNX_Q04917\t113365\t9606.ENSP00000248975\thsa:7533\r\n-P61981\t1433G_HUMAN\t7532\tNP_036611.2\t6016838; 380764684; 635576381; 82407956; 82407958; 550545213; 635576377; 380765197; 82407950; 550545214; 119592210; 1006588564; 1006588561; 635576379; 21464101; 82407952; 48428721; 5726310; 550545212; 635576378; 1006588559; 18088513; 49456805; 1006588565; 550545215; 1006588558; 49456763; 1006588562; 82407948; 82407954; 635576376; 635576380\t2B05:A; 2B05:B; 2B05:C; 2B05:D; 2B05:E; 2B05:F; 3UZD:A; 4E2E:A; 4J6S:A; 4J6S:B; 4J6S:C; 4J6S:D; 4O46:A; 4O46:B; 4O46:C; 4O46:D; 4O46:E; 4O46:F; 5D3E:A; 5D3E:B; 5D3E:E; 5D3E:F; 5D3E:I; 5D3E:J; 6BYJ:A; 6BYJ:B; 6BYJ:C; 6BYJ:D; 6BYJ:E; 6BYJ:F; 6BYL:A; 6BYL:B; 6BYL:C; 6BYL:D; 6BYL:E; 6BYL:F; 6BZD:A; 6BZD:B; 6BZD:C; 6BZD:D; 6FEL:A; 6FEL:B; 6FEL:C; 6FEL:D\tGO:0005829; GO:0070062; GO:0005925; GO:0016020; GO:0005739; GO:0043209; GO:0042802; GO:0005159; GO:0019904; GO:0005080; GO:0008426; GO:0030971; GO:0003723; GO:0032869; GO:0097711; GO:0000086; GO:0061024; GO:0006469; GO:1900740; GO:0006605; GO:0010389; GO:0045664; GO:0009966; GO:0048167\t\t605356; 617665\tHs.744840\tENSG00000170027\tENST00000307630\tENSP00000306330\tNX_P61981\t113364\t9606.ENSP00000306330\thsa:7532\r\n-P31947\t1433S_HUMAN\t2810\tNP_006133.1\t436408756; 306991738; 969812714; 350610438; 350610440; 2702355; 393715161; 394985958; 398953; 305677674; 305677670; 350610436; 528082005; 390981001; 1025734704; 187302; 12654345'..b'BYU9\tH9BYU9_HUMAN\t\t\t380509482\t\t\t\t\tHs.656020; Hs.743218\t\t\t\t\t\t\t\r\n-L0BXM2\tL0BXM2_HUMAN\t\t\t429509581\t\t\t\t\tHs.654404; Hs.726974; Hs.77961\t\t\t\t\t\t\t\r\n-O02929\tO02929_HUMAN\t\t\t2911696\t\t\t\t\tHs.512152\t\t\t\t\t\t\t\r\n-Q5J1K7\tQ5J1K7_HUMAN\t\t\t48525620\t\tGO:0016740\t\t\tHs.24976; Hs.731997\t\t\t\t\t\t\t\r\n-B4E318\tB4E318_HUMAN\t\t\t194385910\t\tGO:0005634; GO:0007049; GO:0006281\t\t\tHs.370292; Hs.715543\t\t\t\t\t\t\t\r\n-D5FI12\tD5FI12_HUMAN\t\t\t226525144\t\t\t\t\t\t\t\t\t\t\t\t\r\n-D5FZK3\tD5FZK3_HUMAN\t\t\t227344687\t\t\t\t\tHs.654404; Hs.726974; Hs.77961\t\t\t\t\t\t\t\r\n-D5FZV1\tD5FZV1_HUMAN\t\t\t227344905\t\t\t\t\t\t\t\t\t\t\t\t\r\n-D6MJ84\tD6MJ84_HUMAN\t\t\t284944706\t\t\t\t\tHs.181244; Hs.713441\t\t\t\t\t\t\t\r\n-A0A0A7C4S6\tA0A0A7C4S6_HUMAN\t\t\t627793257\t\t\t\t\tHs.654404; Hs.726974; Hs.77961\t\t\t\t\t\t\t\r\n-B7Z1W6\tB7Z1W6_HUMAN\t84172\tNP_001269706.1; NP_001269708.1; NP_061887.2\t33469941; 544346144; 544346184; 221039778\t\tGO:0005634; GO:0003677; GO:0003899; GO:0032549; GO:0006351\t\t\tHs.745127\t\t\t\t\t\t\thsa:84172\r\n-B7Z3I6\tB7Z3I6_HUMAN\t\t\t221041090\t\tGO:0005874; GO:0005524; GO:0008569; GO:0008017; GO:0007018\t\t\tHs.23131\t\t\t\t\t\t\t\r\n-B7Z726\tB7Z726_HUMAN\t\t\t221043570\t\t\t\t\tHs.654350\t\t\t\t\t\t\t\r\n-B8Y6A4\tB8Y6A4_HUMAN\t\t\t219693185\t\t\t\t\tHs.654404; Hs.726974; Hs.77961\t\t\t\t\t\t\t\r\n-G0KXI6\tG0KXI6_HUMAN\t\t\t255688302\t\t\t\t\t\t\t\t\t\t\t\t\r\n-G3D6D0\tG3D6D0_HUMAN\t\t\t341835944\t\t\t\t\tHs.656020; Hs.743218\t\t\t\t\t\t\t\r\n-K4MMM0\tK4MMM0_HUMAN\t\t\t409191781\t\tGO:0016021; GO:0016758; GO:0005975\t\t\tHs.654423\t\t\t\t\t\t\t\r\n-Q7Z330\tQ7Z330_HUMAN\t57563\tNP_001278932.1; NP_001278935.1; NP_001278936.1; NP_065854.3\t34101268; 635172825; 635172847; 31874617; 635172838\t\tGO:0031463; GO:0016567\t\t\tHs.106601\t\t\t\t\t\t\thsa:57563\r\n-Q7Z599\tQ7Z599_HUMAN\t57379\tNP_001317272.1; NP_065712.1\t1057867551; 33145979; 10190700\t\tGO:0016814; GO:0008270\t\t\tHs.149342\t\t\t\t\t\t\thsa:57379\r\n-Q86V63\tQ86V63_HUMAN\t\t\t30387865\t\t\t\t\tHs.187861; Hs.713754\t\t\t\t\t\t\t\r\n-Q8IX79\tQ8IX79_HUMAN\t\t\t27462252\t\t\t\t\tHs.467587; Hs.523572; Hs.714127; Hs.721588; Hs.732154; Hs.745004\t\t\t\t\t\t\t\r\n-Q96CD8\tQ96CD8_HUMAN\t\t\t15680095\t\tGO:0005525\t\t\tHs.535192; Hs.586423; Hs.745122\t\t\t\t\t\t\t\r\n-Q9BTM2\tQ9BTM2_HUMAN\t\t\t31455219\t\t\t\t\tHs.26899\t\t\t\t\t\t\t\r\n-A0A0A7C5A4\tA0A0A7C5A4_HUMAN\t\t\t627793153\t\t\t\t\tHs.654404; Hs.726974; Hs.77961\t\t\t\t\t\t\t\r\n-A0A0A7C5U7\tA0A0A7C5U7_HUMAN\t\t\t553561; 38635919; 627793964; 553542\t\tGO:0042613; GO:0019882; GO:0006955\t\t\tHs.485130\t\t\t\t\t\t\t\r\n-A0A0A7C7A9\tA0A0A7C7A9_HUMAN\t\t\t627794195\t\tGO:0042613; GO:0019882; GO:0006955\t\t\tHs.485130\t\t\t\t\t\t\t\r\n-A0A0A7C7J5\tA0A0A7C7J5_HUMAN\t\t\t627794375\t\tGO:0042613; GO:0019882; GO:0006955\t\t\t\t\t\t\t\t\t\t\r\n-A0A0A7C7V5\tA0A0A7C7V5_HUMAN\t\t\t627794597\t\tGO:0042613; GO:0019882; GO:0006955\t\t\tHs.409934; Hs.534322\t\t\t\t\t\t\t\r\n-A0A0A7C915\tA0A0A7C915_HUMAN\t\t\t628821314\t\t\t\t\tHs.181244; Hs.713441\t\t\t\t\t\t\t\r\n-A0A0A7C9G9\tA0A0A7C9G9_HUMAN\t\t\t628822025\t\tGO:0042613; GO:0019882; GO:0006955\t\t\tHs.485130\t\t\t\t\t\t\t\r\n-A0A0A7C9W7\tA0A0A7C9W7_HUMAN\t\t\t628821876\t\t\t\t\tHs.656020; Hs.743218\t\t\t\t\t\t\t\r\n-A0A0A7CAK0\tA0A0A7CAK0_HUMAN\t\t\t628822922\t\tGO:0042613; GO:0019882; GO:0006955\t\t\tHs.409934; Hs.534322\t\t\t\t\t\t\t\r\n-A2V815\tA2V815_HUMAN\t\t\t124517293\t\t\t\t\tHs.181244; Hs.713441\t\t\t\t\t\t\t\r\n-E0X602\tE0X602_HUMAN\t\t\t294357060\t\t\t\t\t\t\t\t\t\t\t\t\r\n-G1EMS6\tG1EMS6_HUMAN\t\t\t341835500\t\t\t\t\tHs.656020; Hs.743218\t\t\t\t\t\t\t\r\n-G1EPG1\tG1EPG1_HUMAN\t\t\t341838574\t\t\t\t\tHs.181244; Hs.713441\t\t\t\t\t\t\t\r\n-G1EQ22\tG1EQ22_HUMAN\t\t\t341838996\t\t\t\t\tHs.654404; Hs.726974; Hs.77961\t\t\t\t\t\t\t\r\n-A2NW97\tA2NW97_HUMAN\t\t\t33287; 107596\t\t\tS21916\t\t\t\t\t\t\t\t\t\r\n-B7Z3Z2\tB7Z3Z2_HUMAN\t\t\t221041402\t\tGO:0005622; GO:0005089; GO:0035556; GO:0035023\t\t\tHs.387262\t\t\t\t\t\t\t\r\n-B7Z5Z9\tB7Z5Z9_HUMAN\t\t\t221042816\t\tGO:0005525; GO:0003924\t\t\tHs.503222; Hs.591552\t\t\t\t\t\t\t\r\n-B7Z615\tB7Z615_HUMAN\t\t\t221042848\t\tGO:0045892\t\t\t\t\t\t\t\t\t\t\r\n-B7Z6U6\tB7Z6U6_HUMAN\t\t\t221043410\t\tGO:0008305; GO:0038023; GO:0007160; GO:0007229\t\t\tHs.654470\t\t\t\t\t\t\t\r\n-O95088\tO95088_HUMAN\t\t\t4102737\t\tGO:0016021\t\t\tHs.534667\t\t\t\t\t\t\t\r\n-O95325\tO95325_HUMAN\t\t\t3859988\t\tGO:0000502; GO:0030234; GO:0042176\t\t\tHs.12970\t\t\t\t\t\t\t\r\n-Q1M2P6\tQ1M2P6_HUMAN\t\t\t33621418\t\t\t\t\t\t\t\t\t\t\t\t\r\n-Q8N5S0\tQ8N5S0_HUMAN\t389199\tNP_981968.1\t44662803; 21594931\t\t\t\t\tHs.375210\t\t\t\t\t\t\thsa:389199\r\n-Q8NH58\tQ8NH58_HUMAN\t\t\t28798457; 21928362\t\tGO:0016021; GO:0005886; GO:0004930; GO:0004984\t\t\t\t\t\t\t\t\t\t\r\n-Q9UNB6\tQ9UNB6_HUMAN\t\t\t5730904\t\t\t\t\tHs.512572; Hs.731378\t\t\t\t\t\t\t\r\n' |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool-data/id_mapping.loc.sample --- a/tool-data/id_mapping.loc.sample Wed Sep 19 04:45:04 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -#This file lists the locations of reference file for id_converter tool -human_id_mapping Human (homo sapiens) tool-data/human_id_mapping_file.tsv -mouse_id_mapping Mouse (Mus musculus) tool-data/mouse_id_mapping.tsv - |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool-data/mouse_id_mapping.tsv --- a/tool-data/mouse_id_mapping.tsv Wed Sep 19 04:45:04 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,83938 +0,0 @@\n-UniProt-AC\tUniProt-ID\tGeneID\tRefSeq\tGI\tPDB\tGO\tPIR\tMIM\tUniGene\tEnsembl_Gene\tEnsembl_Transcript\tEnsembl_Protein\tBioGrid\tSTRING\tKEGG\r\n-Q9CQV8\t1433B_MOUSE\t54401\tNP_061223.2; XP_006499972.1\t1009083986; 409974018; 74219534; 31543974; 3065925; 568917832; 18202836; 74191394\t4GNT:A; 5F74:A; 5WFX:A; 5WFX:B\tGO:0005737; GO:0005829; GO:0042470; GO:0005634; GO:0048471; GO:0032991; GO:0017053; GO:0019899; GO:0042826; GO:0042802; GO:0051219; GO:0050815; GO:0008022; GO:0019904; GO:0044877; GO:0003714; GO:0051220; GO:0045744; GO:0035308; GO:0045892; GO:0043085; GO:0051291; GO:0006605\t\t\tMm.34319; Mm.491117\tENSMUSG00000018326\tENSMUST00000018470\tENSMUSP00000018470\t207648\t10090.ENSMUSP00000018470\tmmu:54401\r\n-P62259\t1433E_MOUSE\t22627\tNP_033562.3\t60391192; 226874906\t\tGO:0030424; GO:0090724; GO:0005737; GO:0005829; GO:0005871; GO:0042470; GO:0005739; GO:0005634; GO:0005886; GO:0005246; GO:0019899; GO:0042826; GO:0042802; GO:0044325; GO:0051219; GO:0050815; GO:0015459; GO:0019904; GO:0046982; GO:0044877; GO:0097110; GO:0031625; GO:0034605; GO:0021987; GO:0021766; GO:0000165; GO:1905913; GO:1901020; GO:1902309; GO:0035308; GO:0001764; GO:0046827; GO:0034504; GO:0006605; GO:0051480; GO:0060306; GO:1901016\tI48337\t\tMm.234700; Mm.471625\tENSMUSG00000020849\tENSMUST00000067664\tENSMUSP00000070993\t204619\t10090.ENSMUSP00000070993\tmmu:22627\r\n-P68510\t1433F_MOUSE\t22629\tNP_035868.1\t74226056; 17976969; 1526541; 74139366; 74140682; 3335652; 55976655; 1354808; 26346472; 74214318; 148705461; 38181914; 14198255; 6756037\t5YQG:A; 5YQG:B; 5YQG:C; 5YQG:D\tGO:0005737; GO:0005829; GO:0014704; GO:0005886; GO:0003779; GO:0019899; GO:0035259; GO:0042802; GO:0044325; GO:0019904; GO:0046982; GO:0017080; GO:0007010; GO:0006713; GO:0042921; GO:0006886; GO:0086010; GO:0043066; GO:0050774; GO:0045893; GO:0007088; GO:2000649; GO:0002028\t\t\tMm.332314\tENSMUSG00000018965\tENSMUST00000019109\tENSMUSP00000019109\t204621\t10090.ENSMUSP00000019109\tmmu:22629\r\n-P61982\t1433G_MOUSE\t22628\tNP_061359.2\t74215924; 31543976; 48428722; 3065929\t\tGO:0005829; GO:0043209; GO:0031982; GO:0003779; GO:0042802; GO:0005159; GO:0019904; GO:0005080; GO:0030971; GO:0032869; GO:0006605; GO:0045664; GO:0048167\t\t\tMm.233813\tENSMUSG00000051391\tENSMUST00000055808; ENSMUST00000198270\tENSMUSP00000051223; ENSMUSP00000143631\t204620\t10090.ENSMUSP00000051223\tmmu:22628\r\n-O70456\t1433S_MOUSE\t55948\tNP_061224.2\t148698109; 18202125; 74138801; 134023662; 338817846; 74142094; 3065927\t\tGO:0005737; GO:0005829; GO:0005576; GO:0005634; GO:0042802; GO:0051219; GO:0019904; GO:0019901; GO:0061436; GO:0008630; GO:0031424; GO:0003334; GO:0030216; GO:0043154; GO:0010839; GO:0030307; GO:0045606; GO:0046827; GO:0051726; GO:0000079; GO:0010482; GO:0001836; GO:0043588\t\t\tMm.44482\tENSMUSG00000047281\tENSMUST00000057311\tENSMUSP00000050374\t207743\t10090.ENSMUSP00000050374\tmmu:55948\r\n-P68254\t1433T_MOUSE\t22630\tNP_035869.1\t68566157; 74226957; 74204655; 6756039; 51593617; 55153870\t\tGO:0005737; GO:0005829; GO:0032991; GO:0071889; GO:0042802; GO:0044325; GO:0008022; GO:0019904; GO:0047485; GO:0034766; GO:0045892; GO:0006605; GO:0007165; GO:0007264\t\t\tMm.289630\tENSMUSG00000076432\tENSMUST00000049531; ENSMUST00000103002\tENSMUSP00000106602; ENSMUSP00000100067\t204622\t10090.ENSMUSP00000100067\tmmu:22630\r\n-P63101\t1433Z_MOUSE\t22631\tNP_001240734.1; NP_001240735.1; NP_035870.1; XP_011243654.1\t74147004; 29748002; 74189019; 1304166; 1841387; 59808984; 74219475; 359385696; 74216901; 52000885; 1526539; 74207182; 1711130; 755550334; 148676867; 359385698; 26350495; 6756041; 74187552\t\tGO:0031252; GO:0005829; GO:0042629; GO:0042470; GO:0005739; GO:0005634; GO:0048471; GO:0014069; GO:0032991; GO:0042802; GO:0044325; GO:0019904; GO:0019901; GO:0044877; GO:0008134; GO:0031625; GO:0051683; GO:0090168; GO:0002553; GO:0006605; GO:0006626; GO:0010941; GO:0042493\tJC5384\t\tMm.3360\tENSMUSG00000022285\tENSMUST00000022894; ENSMUST00000110361; ENSMUST00000110362\tENSMUSP00000022894; ENSMUSP00000105990; ENSMUSP00000105991\t204623\t10090.ENSMUSP00000022894\tmmu:22631\r\n-A2AIG8\t1A1L1_MOUS'..b'; NP_032011.2\t1109303211; 111185909; 545478697; 1109303237; 74150968\t\tGO:0006281\t\t\tMm.126106; Mm.465019\t\t\t\t\t\tmmu:14088\r\n-Q3UIC2\tQ3UIC2_MOUSE\t12558\tNP_031690.3\t161760627; 74150890\t\tGO:0016021; GO:0005886; GO:0005509; GO:0007156; GO:0009966\t\t\tMm.257437\t\t\t\t\t\tmmu:12558\r\n-Q3UK70\tQ3UK70_MOUSE\t\t\t74222256\t\tGO:0015935; GO:0003723; GO:0003735; GO:0006412\t\t\tMm.643\t\t\t\t\t\t\r\n-Q3UMD2\tQ3UMD2_MOUSE\t\t\t74201476\t\t\t\t\tMm.245085\t\t\t\t\t\t\r\n-Q3UNQ3\tQ3UNQ3_MOUSE\t\t\t74184311\t\t\t\t\tMm.28265\t\t\t\t\t\t\r\n-Q3UU25\tQ3UU25_MOUSE\t319493\tNP_001028550.2\t74218427; 283837884\t\t\t\t\tMm.234565\t\t\t\t\t\tmmu:319493\r\n-Q3UX09\tQ3UX09_MOUSE\t194227\tNP_001007078.2\t74193576; 227496213\t\tGO:0043066; GO:0045596; GO:0045892; GO:0008284\t\t\tMm.371676\t\t\t\t\t\tmmu:194227\r\n-Q3UZ51\tQ3UZ51_MOUSE\t\t\t74137263\t\tGO:0003676\t\t\tMm.392436; Mm.436917; Mm.436932\t\t\t\t\t\t\r\n-B7ZN55\tB7ZN55_MOUSE\t\t\t219841786\t\tGO:0016021\t\t\tMm.491229\t\t\t\t\t\t\r\n-G3UZB0\tG3UZB0_MOUSE\t\t\t\t\tGO:0035097; GO:0060717; GO:0071557; GO:0048304; GO:2001022; GO:1902749\t\t\t\tENSMUSG00000030680\tENSMUST00000162069\tENSMUSP00000123889\t\t\t\r\n-Q3TXM9\tQ3TXM9_MOUSE\t\t\t74192738\t\tGO:0003723\t\t\tMm.287826\t\t\t\t\t\t\r\n-Q3TZ04\tQ3TZ04_MOUSE\t13972\tNP_001272422.1; XP_011244131.1; XP_011244132.1\t755553181; 74196585; 550822226; 755553179\t\t\t\t\tMm.236139\t\t\t\t\t\t\r\n-Q3U4R9\tQ3U4R9_MOUSE\t\t\t74180399\t\t\t\t\tMm.217161; Mm.446592\t\t\t\t\t\t\r\n-Q3UN94\tQ3UN94_MOUSE\t\t\t74188436\t\tGO:0016021\t\t\tMm.151098\t\t\t\t\t\t\r\n-Q3UUK3\tQ3UUK3_MOUSE\t\t\t74209842\t\tGO:0016021; GO:0038036\t\t\tMm.982\t\t\t\t\t\t\r\n-Q3V322\tQ3V322_MOUSE\t\t\t74193499\t\t\t\t\tMm.290182\t\t\t\t\t\t\r\n-Q3V394\tQ3V394_MOUSE\t\t\t74193339\t\tGO:0016021; GO:0005215; GO:0006814; GO:0055085\t\t\tMm.340778\t\t\t\t\t\t\r\n-A2NV19\tA2NV19_MOUSE\t\t\t110358; 53214\t\t\tS09259\t\tMm.333124; Mm.489779\t\t\t\t\t\t\r\n-B7ZN90\tB7ZN90_MOUSE\t\t\t219518525\t\tGO:0008305; GO:0007155; GO:0007229\t\t\tMm.1618\t\t\t\t\t\t\r\n-O88715\tO88715_MOUSE\t\t\t3559944; 81861528\t\t\t\t\tMm.334332\t\t\t\t\t\t\r\n-Q3T9Y6\tQ3T9Y6_MOUSE\t\t\t74186170\t\t\t\t\tMm.483595\t\t\t\t\t\t\r\n-Q3TA76\tQ3TA76_MOUSE\t\t\t74182277\t\t\t\t\tMm.130902\t\t\t\t\t\t\r\n-Q3TFK2\tQ3TFK2_MOUSE\t236733\tNP_663603.3\t164663834; 74139517\t\tGO:0036459; GO:0016579; GO:0006511\t\t\tMm.34489\t\t\t\t\t\tmmu:236733\r\n-Q3TP78\tQ3TP78_MOUSE\t\t\t74218995\t\tGO:0004725\t\t\tMm.258771\t\t\t\t\t\t\r\n-Q3TQJ9\tQ3TQJ9_MOUSE\t\t\t74201000\t\tGO:0046332; GO:0000122; GO:0030512\t\t\tMm.15406; Mm.491655\t\t\t\t\t\t\r\n-Q3TSP0\tQ3TSP0_MOUSE\t\t\t74183580\t\tGO:0004719\t\t\tMm.21539\t\t\t\t\t\t\r\n-Q3U0F8\tQ3U0F8_MOUSE\t\t\t74142717\t\tGO:0016589; GO:0005524; GO:0016887; GO:0003677; GO:0004386; GO:0031491; GO:0043044\t\t\tMm.246803; Mm.474173\t\t\t\t\t\t\r\n-Q3UH17\tQ3UH17_MOUSE\t14268\tNP_001263341.1\t74188584; 449083345\t\tGO:0005576\t\t\tMm.193099\t\t\t\t\t\t\r\n-Q9ESQ6\tQ9ESQ6_MOUSE\t\t\t81868400; 9971585\t\t\t\t\tMm.2339\t\t\t\t\t\t\r\n-A8E635\tA8E635_MOUSE\t\t\t157743058\t\tGO:0032580; GO:0008376\t\t\tMm.333916\t\t\t\t\t\t\r\n-F1ABS2\tF1ABS2_MOUSE\t\t\t322718486\t\t\t\t\tMm.3383\t\t\t\t\t\t\r\n-Q6LCE8\tQ6LCE8_MOUSE\t\t\t81863851; 2511434\t\t\t\t\tMm.244820\t\t\t\t\t\t\r\n-Q8BK89\tQ8BK89_MOUSE\t\t\t26344423; 81896459\t\tGO:0005874; GO:0007017\t\t\tMm.379227; Mm.472121\t\t\t\t\t\t\r\n-Q8C316\tQ8C316_MOUSE\t\t\t81876264; 26352424\t\tGO:0005811\t\t\tMm.488086; Mm.490271\t\t\t\t\t\t\r\n-X5J546\tX5J546_MOUSE\t\t\t602615842\t\t\t\t\t\t\t\t\t\t\t\r\n-Q8BNW5\tQ8BNW5_MOUSE\t\t\t81913447; 26348343\t\tGO:0005622; GO:0004715; GO:0035556\t\t\tMm.504\t\t\t\t\t\t\r\n-X5J4P1\tX5J4P1_MOUSE\t\t\t602617091\t\t\t\t\t\t\t\t\t\t\t\r\n-X5J4Y9\tX5J4Y9_MOUSE\t\t\t602617005\t\t\t\t\t\t\t\t\t\t\t\r\n-A0A2I3BPU5\tA0A2I3BPU5_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000033595\tENSMUST00000226548\tENSMUSP00000153920\t\t\t\r\n-A0A2I3BRV4\tA0A2I3BRV4_MOUSE\t\t\t\t\tGO:0016021; GO:0005886; GO:0004930; GO:0004984; GO:0007186; GO:0007608\t\t\t\tENSMUSG00000107822\tENSMUST00000204477\tENSMUSP00000154751\t\t\t\r\n-A0A1L1STZ9\tA0A1L1STZ9_MOUSE\t258235\tNP_997018.2\t120953202\t\tGO:0016021; GO:0005886; GO:0004930; GO:0004984; GO:0007186; GO:0007608\t\t\tMm.314795\tENSMUSG00000110804\tENSMUST00000216851\tENSMUSP00000150546\t\t\tmmu:258235\r\n-A0A1S6GWH8\tA0A1S6GWH8_MOUSE\t\t\t1148885665\t\tGO:0005846; GO:0005634; GO:0000339; GO:0045292\t\t\tMm.290027; Mm.456900\t\t\t\t\t\t\r\n-A0A1Y7VNR1\tA0A1Y7VNR1_MOUSE\t\t\t\t\tGO:0047023; GO:0016229\t\t\t\tENSMUSG00000033715\tENSMUST00000147180\tENSMUSP00000152562\t\t\t\r\n-A0A1W2P6G7\tA0A1W2P6G7_MOUSE\t432450\tXP_011241491.1\t755533138\t\tGO:0016021\t\t\tMm.49665\tENSMUSG00000069670\tENSMUST00000218645\tENSMUSP00000151255\t\t\t\r\n' |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool-data/mouse_id_mapping_23-10-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mouse_id_mapping_23-10-2018.tsv Tue Dec 18 09:57:21 2018 -0500 |
| b |
| b'@@ -0,0 +1,84835 @@\n+UniProt-AC\tUniProt-ID\tGeneID\tRefSeq\tGI\tPDB\tGO\tPIR\tMIM\tUniGene\tEnsembl_Gene\tEnsembl_Transcript\tEnsembl_Protein\tBioGrid\tSTRING\tKEGG\r\n+Q9CQV8\t1433B_MOUSE\t54401\tNP_061223.2; XP_006499972.1\t1009083986; 409974018; 74219534; 31543974; 3065925; 568917832; 18202836; 74191394\t4GNT:A; 5F74:A; 5WFU:A; 5WFU:B; 5WFU:C; 5WFU:D; 5WFX:A; 5WFX:B\tGO:0005737; GO:0005829; GO:0042470; GO:0005634; GO:0048471; GO:0032991; GO:0017053; GO:0019899; GO:0042826; GO:0042802; GO:0051219; GO:0050815; GO:0008022; GO:0019904; GO:0044877; GO:0003714; GO:0051220; GO:0045744; GO:0035308; GO:0045892; GO:0043085; GO:0051291; GO:0006605\t\t\tMm.34319; Mm.491117\tENSMUSG00000018326\tENSMUST00000018470\tENSMUSP00000018470\t207648\t10090.ENSMUSP00000018470\tmmu:54401\r\n+P62259\t1433E_MOUSE\t22627\tNP_033562.3\t60391192; 226874906\t\tGO:0030424; GO:0090724; GO:0005737; GO:0005829; GO:0098978; GO:0005871; GO:0042470; GO:0005739; GO:0005634; GO:0005886; GO:0005246; GO:0019899; GO:0042826; GO:0042802; GO:0044325; GO:0051219; GO:0050815; GO:0015459; GO:0019904; GO:0046982; GO:0044877; GO:0097110; GO:0031625; GO:0034605; GO:0021987; GO:0021766; GO:0000165; GO:1905913; GO:1901020; GO:1902309; GO:0035308; GO:0001764; GO:0046827; GO:0034504; GO:0006605; GO:0051480; GO:0060306; GO:0099072; GO:1901016\tI48337\t\tMm.234700; Mm.471625\tENSMUSG00000020849\tENSMUST00000067664\tENSMUSP00000070993\t204619\t10090.ENSMUSP00000070993\tmmu:22627\r\n+P68510\t1433F_MOUSE\t22629\tNP_035868.1\t74226056; 17976969; 1526541; 74139366; 74140682; 3335652; 55976655; 1354808; 26346472; 74214318; 148705461; 38181914; 14198255; 6756037\t5YQG:A; 5YQG:B; 5YQG:C; 5YQG:D\tGO:0005737; GO:0005829; GO:0014704; GO:0005886; GO:0003779; GO:0019899; GO:0035259; GO:0042802; GO:0044325; GO:0019904; GO:0046982; GO:0017080; GO:0007010; GO:0006713; GO:0042921; GO:0006886; GO:0086010; GO:0043066; GO:0050774; GO:0045893; GO:0007088; GO:2000649; GO:0002028\t\t\tMm.332314\tENSMUSG00000018965\tENSMUST00000019109\tENSMUSP00000019109\t204621\t10090.ENSMUSP00000019109\tmmu:22629\r\n+P61982\t1433G_MOUSE\t22628\tNP_061359.2\t74215924; 31543976; 48428722; 3065929\t\tGO:0005829; GO:0043209; GO:0098793; GO:0031982; GO:0003779; GO:0042802; GO:0005159; GO:0019904; GO:0005080; GO:0030971; GO:0032869; GO:0006605; GO:0045664; GO:0048167\t\t\tMm.233813\tENSMUSG00000051391\tENSMUST00000055808; ENSMUST00000198270\tENSMUSP00000051223; ENSMUSP00000143631\t204620\t10090.ENSMUSP00000051223\tmmu:22628\r\n+O70456\t1433S_MOUSE\t55948\tNP_061224.2\t148698109; 18202125; 74138801; 134023662; 338817846; 74142094; 3065927\t\tGO:0005737; GO:0005829; GO:0005576; GO:0005634; GO:0042802; GO:0051219; GO:0019904; GO:0019901; GO:0061436; GO:0008630; GO:0031424; GO:0003334; GO:0030216; GO:0043154; GO:0010839; GO:0030307; GO:0045606; GO:0046827; GO:0051726; GO:0000079; GO:0010482; GO:0001836; GO:0043588\t\t\tMm.44482\tENSMUSG00000047281\tENSMUST00000057311\tENSMUSP00000050374\t207743\t10090.ENSMUSP00000050374\tmmu:55948\r\n+P68254\t1433T_MOUSE\t22630\tNP_035869.1\t68566157; 74226957; 74204655; 6756039; 51593617; 55153870\t\tGO:0005737; GO:0005829; GO:0032991; GO:0071889; GO:0042802; GO:0044325; GO:0008022; GO:0019904; GO:0047485; GO:0034766; GO:0045892; GO:0006605; GO:0007165; GO:0007264\t\t\tMm.289630\tENSMUSG00000076432\tENSMUST00000103002; ENSMUST00000135088; ENSMUST00000155480\tENSMUSP00000100067; ENSMUSP00000123605; ENSMUSP00000117118\t204622\t10090.ENSMUSP00000100067\tmmu:22630\r\n+P63101\t1433Z_MOUSE\t22631\tNP_001240734.1; NP_001240735.1; NP_035870.1; XP_011243654.1\t74147004; 29748002; 74189019; 1304166; 1841387; 59808984; 74219475; 359385696; 74216901; 52000885; 1526539; 74207182; 1711130; 755550334; 148676867; 359385698; 26350495; 6756041; 74187552\t\tGO:0031252; GO:0005829; GO:0098978; GO:0042629; GO:0042470; GO:0005739; GO:0005634; GO:0048471; GO:0014069; GO:0032991; GO:0042802; GO:0044325; GO:0019904; GO:0019901; GO:0044877; GO:0008134; GO:0031625; GO:0051683; GO:0090168; GO:0002553; GO:0006605; GO:0006626; GO:0010941; GO:0090128; GO:0042493\tJC5384\t\tMm.3360\tENSMUSG00000022285\tENSMUST00000022894; ENSMUST00000110361; ENSMUST'..b'469497\t\tGO:0016021; GO:0030246\t\t\tMm.30870\t\t\t\t\t\t\r\n+A6NAU2\tA6NAU2_MOUSE\t\t\t148923137\t\t\t\t\tMm.396155; Mm.443041; Mm.445125; Mm.483675\t\t\t\t\t\t\r\n+Q35035\tQ35035_MOUSE\t\t\t342558; 81887144\t\tGO:0016021; GO:0005739\t\t\t\t\t\t\t\t\t\r\n+Q62183\tQ62183_MOUSE\t\t\t81863069; 53992\t\t\tF39487; S26410\t\tMm.264651; Mm.432087\t\t\t\t\t\t\r\n+Q6UL10\tQ6UL10_MOUSE\t\t\t37675525; 81864302\t\t\t\t\tMm.203866; Mm.392302\t\t\t\t\t\t\r\n+Q3UBW3\tQ3UBW3_MOUSE\t\t\t74178127\t\tGO:0016021; GO:0005741; GO:0006886\t\t\tMm.246435; Mm.485795\t\t\t\t\t\t\r\n+A0A0U1RNQ2\tA0A0U1RNQ2_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000040940\tENSMUST00000206028\tENSMUSP00000145659\t\t\t\r\n+A0A0U1RPE1\tA0A0U1RPE1_MOUSE\t\t\t\t\tGO:0010494; GO:0005634; GO:0017091; GO:0007281; GO:0008284; GO:0017145\t\t\t\tENSMUSG00000030846\tENSMUST00000133444\tENSMUSP00000145943\t\t\t\r\n+A0A0U1RPT9\tA0A0U1RPT9_MOUSE\t\t\t\t\tGO:0000124\t\t\t\tENSMUSG00000030714\tENSMUST00000205507\tENSMUSP00000146122\t\t\t\r\n+F8WHN2\tF8WHN2_MOUSE\t52609\tXP_006521207.1\t568992809\t\tGO:0000792; GO:0035102; GO:0003682; GO:0035064; GO:0003727; GO:0048733\t\t\tMm.323442\tENSMUSG00000053411\tENSMUST00000089293\tENSMUSP00000086708\t\t\t\r\n+I6L9E4\tI6L9E4_MOUSE\t107815\tNP_001277580.1\t594591551; 38614169\t\tGO:0000790; GO:0005634; GO:0001741; GO:0006915; GO:0034613; GO:0036353; GO:0006355\t\t\tMm.159173\t\t\t\t\t\tmmu:107815\r\n+Q14BP4\tQ14BP4_MOUSE\t\t\t109732235\t\tGO:0000932\t\t\tMm.60720\t\t\t\t\t\t\r\n+Q8C5S1\tQ8C5S1_MOUSE\t\t\t26346036; 81876699\t\t\t\t\tMm.8655\t\t\t\t\t\t\r\n+Q99KA3\tQ99KA3_MOUSE\t\t\t13435885; 81903075\t\tGO:0016324; GO:0016323; GO:0098850; GO:0016020; GO:0033180; GO:0008021; GO:0016471; GO:0005524; GO:0044877; GO:0015078; GO:0015991; GO:0055074; GO:0007588; GO:0001503; GO:0045851; GO:1902600; GO:0006885; GO:0007605\t\t\tMm.220823\t\t\t\t\t\t\r\n+M0QWD2\tM0QWD2_MOUSE\t\t\t\t\tGO:0004222; GO:0002949\t\t\t\tENSMUSG00000026096\tENSMUST00000151296\tENSMUSP00000137772\t\t\t\r\n+H3BLE4\tH3BLE4_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000028552\tENSMUST00000177192\tENSMUSP00000135755\t\t\t\r\n+Q53TY6\tQ53TY6_MOUSE\t\t\t81872928; 62945212\t\t\t\t\tMm.28721\t\t\t\t\t\t\r\n+A4FVC9\tA4FVC9_MOUSE\t\t\t133778291\t\tGO:0016021\t\t\tMm.30155; Mm.320896\t\t\t\t\t\t\r\n+Q149G4\tQ149G4_MOUSE\t\t\t109734469\t\tGO:0005887; GO:0008028; GO:1901475\t\t\tMm.29161; Mm.455126; Mm.458462\t\t\t\t\t\t\r\n+Q6W066\tQ6W066_MOUSE\t\t\t81864382; 46518892\t\t\t\t\tMm.377646\t\t\t\t\t\t\r\n+Q8C187\tQ8C187_MOUSE\t\t\t81876027; 26324704\t\tGO:0008234\t\t\tMm.384023; Mm.487443\t\t\t\t\t\t\r\n+Q99LM6\tQ99LM6_MOUSE\t\t\t81903157; 12805659\t\tGO:0016021\t\t\tMm.3815\t\t\t\t\t\t\r\n+S4R176\tS4R176_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000074793\tENSMUST00000127862\tENSMUSP00000138109\t\t\t\r\n+S4R2G5\tS4R2G5_MOUSE\t14447\tNP_001277560.1\t594591567\t\tGO:0004365; GO:0051287; GO:0050661; GO:0006006; GO:0006096\t\t\tMm.436562\tENSMUSG00000061099\tENSMUST00000182634\tENSMUSP00000138634\t\t\t\r\n+V9GXL5\tV9GXL5_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000090626\tENSMUST00000184557\tENSMUSP00000139212\t\t\t\r\n+Q61698\tQ61698_MOUSE\t\t\t387210; 81890208\t\t\t\t\tMm.372314\t\t\t\t\t\t\r\n+Q8BSG4\tQ8BSG4_MOUSE\t\t\t26328753; 81874997\t\t\t\t\tMm.483438\t\t\t\t\t\t\r\n+A0A0U1RQ52\tA0A0U1RQ52_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000055024\tENSMUST00000206833\tENSMUSP00000146251\t\t\t\r\n+H3BJV5\tH3BJV5_MOUSE\t\t\t\t\tGO:0048873; GO:0120162\t\t\t\tENSMUSG00000026526\tENSMUST00000154956\tENSMUSP00000135140\t\t\t\r\n+H3BLS5\tH3BLS5_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000020251\tENSMUST00000125505\tENSMUSP00000135897\t\t\t\r\n+J3KMK8\tJ3KMK8_MOUSE\t\t\t\t\tGO:0004867\t\t\t\tENSMUSG00000074593\tENSMUST00000180193\tENSMUSP00000135911\t\t\t\r\n+W8QPF2\tW8QPF2_MOUSE\t\t\t591402862\t\tGO:0008021; GO:0007269\t\t\tMm.439844\t\t\t\t\t\t\r\n+Q149I9\tQ149I9_MOUSE\t\t\t109734446\t\t\t\t\tMm.443238\t\t\t\t\t\t\r\n+Q14C48\tQ14C48_MOUSE\t\t\t109730769\t\tGO:0005594\t\t\tMm.141312\t\t\t\t\t\t\r\n+Q6UKZ1\tQ6UKZ1_MOUSE\t\t\t40737634; 81893029\t\tGO:0005615; GO:0004867\t\t\tMm.337362\t\t\t\t\t\t\r\n+Q80Y29\tQ80Y29_MOUSE\t\t\t81895390; 29477191\t\tGO:0005615; GO:0004867\t\t\tMm.379809\t\t\t\t\t\t\r\n+S4R2N9\tS4R2N9_MOUSE\t\t\t\t\tGO:0016020; GO:1900383\t\t\t\tENSMUSG00000058589\tENSMUST00000182786\tENSMUSP00000138720\t\t\t\r\n+S4R2Q9\tS4R2Q9_MOUSE\t\t\t\t\t\t\t\t\tENSMUSG00000032826\tENSMUST00000182571\tENSMUSP00000138747\t\t\t\r\n+Q3LG17\tQ3LG17_MOUSE\t\t\t76559764\t\tGO:0016021\t\t\tMm.228798; Mm.488634\t\t\t\t\t\t\r\n+Q9QWH4\tQ9QWH4_MOUSE\t\t\t81907049; 4098156\t\tGO:0016301\t\t\tMm.4733\t\t\t\t\t\t\r\n+A0A0U1RQ35\tA0A0U1RQ35_MOUSE\t\t\t\t\tGO:0035591; GO:0007165\t\t\t\tENSMUSG00000030733\tENSMUST00000206643\tENSMUSP00000146229\t\t\t\r\n' |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool-data/proteore_id_mapping.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_id_mapping.loc.sample Tue Dec 18 09:57:21 2018 -0500 |
| b |
| @@ -0,0 +1,4 @@ +#This file lists the locations of reference file for id_converter tool +human_id_mapping Human (Homo sapiens) tool-data/human_id_mapping_23-10-2018.tsv +mouse_id_mapping Mouse (Mus musculus) tool-data/mouse_id_mapping_23-10-2018.tsv +rat_id_mapping Rat (Rattus norvegicus) tool-data/rat_id_mapping_23-10-2018.tsv |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool-data/rat_id_mapping_23-10-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rat_id_mapping_23-10-2018.tsv Tue Dec 18 09:57:21 2018 -0500 |
| b |
| b'@@ -0,0 +1,36077 @@\n+UniProt-AC\tUniProt-ID\tGeneID\tRefSeq\tGI\tPDB\tGO\tPIR\tMIM\tUniGene\tEnsembl_Gene\tEnsembl_Transcript\tEnsembl_Protein\tBioGrid\tSTRING\tKEGG\r\n+P35213\t1433B_RAT\t56011\tNP_062250.1\t1911805; 265428; 49904289; 9507243; 1345591; 149042981; 402524\t\tGO:0005737; GO:0005829; GO:0042470; GO:0005634; GO:0048471; GO:0032991; GO:0017053; GO:0042826; GO:0042802; GO:0050815; GO:0008022; GO:0019904; GO:0044877; GO:0051220; GO:0045744; GO:0035308; GO:0045892; GO:0043085; GO:0051291; GO:0006605\tA49023\t\tRn.230081; Rn.8653\tENSRNOG00000010945\tENSRNOT00000016981\tENSRNOP00000016981\t248554\t10116.ENSRNOP00000016981\trno:56011\r\n+P62260\t1433E_RAT\t29753\tNP_113791.1\t487918; 149053422; 38648857; 13928824; 1469948; 61216932; 294504\t\tGO:0030424; GO:0090724; GO:0005737; GO:0005829; GO:0005871; GO:0042470; GO:0005634; GO:0005886; GO:0005246; GO:0019899; GO:0042826; GO:0042802; GO:0044325; GO:0050815; GO:0015459; GO:0019904; GO:0046982; GO:0008426; GO:0044877; GO:0097110; GO:0031625; GO:0034605; GO:0021987; GO:0021766; GO:0000165; GO:1905913; GO:1901020; GO:1902309; GO:0001764; GO:0046827; GO:0034504; GO:0006605; GO:0051480; GO:0060306; GO:1901016; GO:0007165\tJX0341\t\tRn.4225\tENSRNOG00000005290\tENSRNOT00000007100\tENSRNOP00000007100\t248364\t10116.ENSRNOP00000007100\trno:29753\r\n+P68511\t1433F_RAT\t25576\tNP_037184.1\t51858611; 398155; 6981710; 55976637; 149047466\t\tGO:0005737; GO:0019904; GO:0017080; GO:0086010; GO:2000649; GO:0002028\tA60031\t\tRn.3324\tENSRNOG00000055471\tENSRNOT00000085735\tENSRNOP00000075701\t247607\t10116.ENSRNOP00000024388\trno:25576\r\n+P61983\t1433G_RAT\t56010\tNP_062249.1; XP_006249246.2\t149063017; 402526; 48428718; 117558830; 265430; 1046854730; 9507245\t\tGO:0005737; GO:0043209; GO:0031982; GO:0003779; GO:0030234; GO:0042802; GO:0005159; GO:0019904; GO:0005080; GO:0030971; GO:0032869; GO:0006605; GO:0045664; GO:0048167; GO:0007165\tB49023\t\tRn.29936\tENSRNOG00000001436\tENSRNOT00000001954; ENSRNOT00000084730\tENSRNOP00000001954; ENSRNOP00000069671\t248553\t10116.ENSRNOP00000001954\trno:56010\r\n+P68255\t1433T_RAT\t25577\tNP_037185.1\t402509; 149051000; 61216933; 6981712; 38383130\t\tGO:0005737; GO:0032991; GO:0071889; GO:0042802; GO:0044325; GO:0008022; GO:0019904; GO:0047485; GO:0034766; GO:0045892\tI52647\t\tRn.2502\tENSRNOG00000051650\tENSRNOT00000077786\tENSRNOP00000072011\t247608\t10116.ENSRNOP00000011501\trno:25577\r\n+P63102\t1433Z_RAT\t25578\tNP_037143.2; XP_006241591.1\t62871703; 294506; 564359766; 62990183; 402511; 52000883; 68085421; 487920; 149066515; 1051270\t\tGO:0031252; GO:0042629; GO:0042470; GO:0005739; GO:0048471; GO:0014069; GO:0032991; GO:0019904; GO:0044877; GO:0002553; GO:0006626; GO:0042493\tJC2502; JC5232; S59915\t\tRn.1292\tENSRNOG00000008195\tENSRNOT00000035628\tENSRNOP00000030885\t247609\t10116.ENSRNOP00000030885\trno:25578\r\n+P22282\t22P1_RAT\t25030\tNP_036850.1\t112720; 205903; 7549742; 299360; 260883; 530167\t\tGO:0005829; GO:0005634; GO:0004869; GO:0030521\tA49304\t\tRn.9977\t\t\t\t\t10116.ENSRNOP00000040184\trno:25030\r\n+P22283\t22P2_RAT\t296229\tNP_954887.1\t41152508; 112721; 205905; 149041137; 56013; 72679563\t\tGO:0005615; GO:0004869; GO:0002020; GO:2000117\tJT0616\t\tRn.43503\t\t\t\t\t10116.ENSRNOP00000043921\trno:296229\r\n+Q80W83\t2A5B_RAT\t309179\tNP_852044.1; XP_008758365.1\t31077118; 672039381; 81873316; 149062165; 60422755; 30575399\t\tGO:0005737; GO:0000159; GO:0019888; GO:0071363; GO:0070317; GO:0071158; GO:0051091; GO:0010976; GO:0051388; GO:0031334; GO:0045944; GO:0050730; GO:0031952; GO:0001932; GO:0010469; GO:0007165\t\t\tRn.40996\tENSRNOG00000021025\tENSRNOT00000028542\tENSRNOP00000028542\t\t10116.ENSRNOP00000065720\trno:309179\r\n+Q4QQT4\t2AAB_RAT\t315648\tNP_001020589.1\t81918149; 70794752; 67678118\t\tGO:0045121; GO:0060561; GO:2001241\t\t\tRn.163017\tENSRNOG00000010922\tENSRNOT00000064290\tENSRNOP00000059428\t\t10116.ENSRNOP00000059428\trno:315648\r\n+P36876\t2ABA_RAT\t117104\tNP_446451.1\t2346992; 206297; 206299; 16758910; 118764362; 543717; 149030346\t\tGO:0005829; GO:0098978; GO:0000159; GO:0051721; GO:0019888; GO:0004722; GO:0044877; GO:0048156; GO:0032502; GO:0000278; GO:0070262; GO:0043278\tA41805\t\tRn.8115'..b'\t\t\t\tRn.58091\tENSRNOG00000024623\tENSRNOT00000089222\tENSRNOP00000071865\t\t\t\r\n+A0A0G2K4H4\tA0A0G2K4H4_RAT\t\t\t\t\tGO:0070286\t\t\t\tENSRNOG00000038600\tENSRNOT00000077719\tENSRNOP00000073044\t\t\t\r\n+A0A0G2K5J3\tA0A0G2K5J3_RAT\t\t\t\t\tGO:0016021; GO:0005741; GO:0005525; GO:0003924; GO:0008053\t\t\t\tENSRNOG00000011057\tENSRNOT00000077170\tENSRNOP00000073448\t\t\t\r\n+A0A0G2K8P5\tA0A0G2K8P5_RAT\t\t\t\t\tGO:0005737; GO:0019904; GO:0015631; GO:0031122; GO:0035021; GO:0031175; GO:0043087; GO:0031110\t\t\t\tENSRNOG00000013657\tENSRNOT00000079262\tENSRNOP00000074686\t\t\t\r\n+A0A0G2KA67\tA0A0G2KA67_RAT\t\t\t\t\t\t\t\t\tENSRNOG00000032471\tENSRNOT00000079169\tENSRNOP00000075281\t\t\t\r\n+A0A0G2KA16\tA0A0G2KA16_RAT\t\t\t\t\tGO:0007276\t\t\t\tENSRNOG00000053267\tENSRNOT00000084788\tENSRNOP00000075218\t\t\t\r\n+A0A0G2KA20\tA0A0G2KA20_RAT\t117020\tXP_006253486.1\t564389922\t\tGO:0005622; GO:0035091; GO:0005089; GO:0035556; GO:0035023\t\t\tRn.81062\tENSRNOG00000028426\tENSRNOT00000087095\tENSRNOP00000075224\t\t\t\r\n+A0A0H2UHC2\tA0A0H2UHC2_RAT\t\t\t\t\tGO:0005829; GO:0005925; GO:0030914; GO:0004402; GO:0003713; GO:0043966\t\t\t\tENSRNOG00000003816\tENSRNOT00000005090\tENSRNOP00000005090\t\t\t\r\n+A0A0G2JXD2\tA0A0G2JXD2_RAT\t\t\t\t\tGO:0005509\t\t\t\tENSRNOG00000055518\tENSRNOT00000077593\tENSRNOP00000070226\t\t\t\r\n+A0A0G2K0J3\tA0A0G2K0J3_RAT\t\t\t\t\tGO:0007165\t\t\t\tENSRNOG00000053288\tENSRNOT00000082181\tENSRNOP00000071472\t\t\t\r\n+A0A0G2K1N4\tA0A0G2K1N4_RAT\t368042\tXP_006231394.1\t564333605\t\tGO:0005524\t\t\tRn.1237\tENSRNOG00000017938\tENSRNOT00000081786\tENSRNOP00000071913\t\t\t\r\n+A0A0G2K2V5\tA0A0G2K2V5_RAT\t\t\t\t\tGO:0098592; GO:0000145; GO:0005886; GO:0017049; GO:0005546; GO:0051601; GO:0006887; GO:0006893; GO:0048015; GO:0050714\t\t\t\tENSRNOG00000002144\tENSRNOT00000090470\tENSRNOP00000072393\t\t\t\r\n+A0A0G2K3K5\tA0A0G2K3K5_RAT\t\t\t\t\tGO:0003945; GO:0030311\t\t\t\tENSRNOG00000008283\tENSRNOT00000079414\tENSRNOP00000072676\t\t\t\r\n+A0A0G2K644\tA0A0G2K644_RAT\t299142\tXP_001077814.1; XP_008762952.1; XP_008774479.1; XP_008774480.1; XP_017449952.1; XP_234300.4\t672056407; 1046893920; 672020832; 672020830; 109479362; 109478281\t\tGO:0005886; GO:0098793; GO:0005509; GO:0030276; GO:0019905; GO:0006887; GO:0006906\t\t\t\tENSRNOG00000056012\tENSRNOT00000088430\tENSRNOP00000073667\t\t10116.ENSRNOP00000012374\trno:299142\r\n+A0A0G2K6Q7\tA0A0G2K6Q7_RAT\t\t\t\t\tGO:0005622; GO:0003729; GO:0006406\t\t\t\tENSRNOG00000034233\tENSRNOT00000080568\tENSRNOP00000073905\t\t\t\r\n+A0A0G2K7C2\tA0A0G2K7C2_RAT\t309523\tXP_006231347.1\t564333484\t\tGO:0005524; GO:0008017; GO:0003777; GO:0007018; GO:0007088\t\t\tRn.208134\tENSRNOG00000018929\tENSRNOT00000085880\tENSRNOP00000074144\t\t\t\r\n+A0A0G2K8J5\tA0A0G2K8J5_RAT\t\t\t\t\t\t\t\t\tENSRNOG00000056845\tENSRNOT00000087749\tENSRNOP00000074631\t\t\t\r\n+A0A0G2K8W6\tA0A0G2K8W6_RAT\t\t\t\t\t\t\t\t\tENSRNOG00000045541\tENSRNOT00000079969\tENSRNOP00000074763\t\t\t\r\n+A0A0H2UHU1\tA0A0H2UHU1_RAT\t\t\t\t\tGO:0005840; GO:0003735; GO:0006412\t\t\t\tENSRNOG00000023385\tENSRNOT00000030761\tENSRNOP00000033369\t\t\t\r\n+A0A0G2JX23\tA0A0G2JX23_RAT\t\t\t\t\tGO:0016021; GO:0004222; GO:0008584\t\t\t\tENSRNOG00000017554\tENSRNOT00000078085\tENSRNOP00000070106\t\t\t\r\n+A0A0G2K232\tA0A0G2K232_RAT\t\t\t\t\t\t\t\t\tENSRNOG00000005233\tENSRNOT00000084875\tENSRNOP00000072085\t\t\t\r\n+A0A0G2K3B3\tA0A0G2K3B3_RAT\t\t\t\t\tGO:0016021; GO:0030246; GO:0009968\t\t\t\tENSRNOG00000051600\tENSRNOT00000078219\tENSRNOP00000072569\t\t\t\r\n+A0A0G2K6X2\tA0A0G2K6X2_RAT\t\t\t\t\tGO:0016021\t\t\t\tENSRNOG00000059768\tENSRNOT00000080997\tENSRNOP00000073976\t\t\t\r\n+A0A0G2K8E0\tA0A0G2K8E0_RAT\t\t\t\t\tGO:0022625; GO:0003735; GO:0006412\t\t\t\tENSRNOG00000061441\tENSRNOT00000087364\tENSRNOP00000074570\t\t\t\r\n+E9PTU4\tE9PTU4_RAT\t24582\tNP_001164071.1\t282158051\t\tGO:0016459; GO:0051015; GO:0005524; GO:0003774\t\t\tRn.94969\tENSRNOG00000057880\tENSRNOT00000084608\tENSRNOP00000074575\t\t\trno:24582\r\n+F1M6L7\tF1M6L7_RAT\t\t\t\t\tGO:0005794; GO:0016021; GO:0008373; GO:0006486\t\t\t\tENSRNOG00000056894\tENSRNOT00000091407\tENSRNOP00000075041\t\t10116.ENSRNOP00000061512\t\r\n+A0A140TAI7\tA0A140TAI7_RAT\t291772\tNP_001093986.1\t451172098\t\tGO:0051260\t\t\tRn.27416\tENSRNOG00000016467\tENSRNOT00000061504\tENSRNOP00000058222\t\t\trno:291772\r\n+A0A140TAC5\tA0A140TAC5_RAT\t\t\t\t\tGO:0005840; GO:0003735; GO:0006412\t\t\t\tENSRNOG00000016220\tENSRNOT00000021725\tENSRNOP00000021725\t\t\t\r\n' |
| b |
| diff -r 659f1248f535 -r b50d913ec067 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Sep 19 04:45:04 2018 -0400 +++ b/tool_data_table_conf.xml.sample Tue Dec 18 09:57:21 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ <tables> <!-- Location of ID Mapping files for id_converter--> - <table name="id_mapping_tab" comment_char="#"> + <table name="proteore_id_mapping" comment_char="#"> <columns>value, name, path</columns> - <file path="tool-data/id_mapping.loc" /> + <file path="tool-data/proteore_id_mapping.loc" /> </table> </tables> \ No newline at end of file |