| Next changeset 1:23671dd35026 (2018-09-19) |
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planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty |
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README.rst peptide_atlas.loc.sample proteore_ms_observation_pepatlas.R proteore_ms_observation_pepatlas.xml test-data/FKW_Lacombe_et_al_2017_OK.txt test-data/Human_Brain_25-07-2018.tsv test-data/Human_CSF_25-07-2018.tsv test-data/Human_Heart_25-07-2018.tsv test-data/Human_Kidney_25-07-2018.tsv test-data/Human_Liver_25-07-2018.tsv test-data/Human_Plasma_25-07-2018.tsv test-data/Human_Urine_25-07-2018.tsv test-data/PeptideAtlas_output.txt tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 97e4d3a43537 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Sep 19 05:16:37 2018 -0400 |
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| @@ -0,0 +1,24 @@ +Wrapper for Number of MS/MS observations in a tissue (from Peptide Atlas) tool +============================================================================== + +**Authors** + +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 + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + +============================================================================== + +Given a list of Uniprot accession number this tool indicates the number of times a protein has(ve) been observed in a given sample using LC-MS/MS proteomics approach. Could be of interest for people who wants to know to what extent a protein is detectable (and to roughly estimate its level) in a given sample using proteomics. Available human biological samples are the following: brain, heart, kidney, liver, plasma, urine and cerebrospinal fluid (CSF). Data were retrieved from Peptide Atlas release (Jan 2018). + +**Input required** + +A list of Uniprot accession number (e.g. Q12860) provided either in the form of a file (if you choose a file, it is necessary to specify the column where are your Uniprot accession number) or in a copy/paste mode. If your input file or list contains other type of IDs, please use the ID_Converter tool to convert yours into Uniprot accession number. + +**Output** + +Additional columns are created for each selected proteomics sample reporting the number of times all peptides corresponding to a protein have been observed by LC-MS/MS according to Peptide Atlas. “NA” means that no information has been reported suggesting that this protein has not been observed in the sample of interest. \ No newline at end of file |
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| diff -r 000000000000 -r 97e4d3a43537 peptide_atlas.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_atlas.loc.sample Wed Sep 19 05:16:37 2018 -0400 |
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| @@ -0,0 +1,5 @@ +#This file lists the locations name and values of reference files +#for number of MS/MS observations in a tissue +#This is a tab separated file (TAB, not 4 spaces !) +# +#<tissue> <name> <value> |
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| diff -r 000000000000 -r 97e4d3a43537 proteore_ms_observation_pepatlas.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteore_ms_observation_pepatlas.R Wed Sep 19 05:16:37 2018 -0400 |
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| @@ -0,0 +1,122 @@ +# 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 <- try(read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = ""),silent=TRUE) + if (!inherits(headers, 'try-error')){ + file + } else { + stop("Your file seems to be empty, 'number of MS/MS observations in a tissue' tool stopped !") + } + #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 <- try(read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = ""),silent=TRUE) + if (!inherits(file, 'try-error')){ + file + } else { + stop("Your file seems to be empty, 'number of MS/MS observations in a tissue' tool stopped !") + } + # Remove empty rows + file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] + } + return(file) +} + +nb_obs_PeptideAtlas <- function(input, atlas_file) { + ## Calculate the sum of n_observations for each ID in input + atlas = readfile(atlas_file, "true") + return(atlas$nb_obs[match(input,atlas$Uniprot_AC)]) +} + +main = function() { + args <- commandArgs(TRUE) + if(length(args)<1) { + args <- c("--help") + } + + # Help section + if("--help" %in% args) { + cat("Selection and Annotation HPA + Arguments: + --input_type: type of input (list of id or filename) + --input: input + --atlas: list of file(s) path to use + --output: text 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 + + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/retrieve_msbased_pepatlas/args.Rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/retrieve_msbased_pepatlas/args.Rda") + + # Extract input + input_type = args$input_type + if (input_type == "list") { + input = strsplit(args$input, "[ \t\n]+")[[1]] + } else if (input_type == "file") { + filename = args$input + ncol = args$column + # Check ncol + if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) { + stop("Please enter an integer for level") + } else { + ncol = as.numeric(gsub("c", "", ncol)) + } + header = args$header + # Get file content + file = readfile(filename, header) + # Extract Protein IDs list + input = c() + for (row in as.character(file[,ncol])) { + input = c(input, strsplit(row, ";")[[1]][1]) + } + } + + output = args$output + + #function to create a list of infos from file path + extract_info_from_path <- function(path) { + file_name=strsplit(tail(strsplit(path,"/")[[1]],n=1),"\\.")[[1]][1] + date=tail(strsplit(file_name,"_")[[1]],n=1) + tissue=paste(strsplit(file_name,"_")[[1]][1:2],collapse="_") + return (c(date,tissue,file_name,path)) + } + + #data_frame building + paths=strsplit(args$atlas,",")[[1]] + tmp <- sapply(paths, extract_info_from_path,USE.NAMES = FALSE) + df <- as.data.frame(t(as.data.frame(tmp)),row.names = c(""),stringsAsFactors = FALSE) + names(df) <- c("date","tissue","filename","path") + + # Annotations + res = sapply(df$path, function(x) nb_obs_PeptideAtlas(input, x), USE.NAMES = FALSE) + names=df$filename + + # Write output + if (input_type == "list") { + res = cbind(as.matrix(input), res) + names = c("Uniprot accession number", names) + colnames(res) = names + write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE) + } else if (input_type == "file") { + names = c(names(file), names) + output_content = cbind(file, res) + colnames(output_content) = names + write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE) + } +} + +main() +#Rscript retrieve_peptideatlas.R --input_type="file" --input="test-data/FKW_Lacombe_et_al_2017_OK.txt" --atlas_brain="Human_Brain_201803_PeptideAtlas.txt" --column="c1" --header="true" --output="test-data/PeptideAtlas_output.txt" --atlas_urine="Human_Urine_201803_PeptideAtlas.txt" --atlas="brain,urine" + |
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| diff -r 000000000000 -r 97e4d3a43537 proteore_ms_observation_pepatlas.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteore_ms_observation_pepatlas.xml Wed Sep 19 05:16:37 2018 -0400 |
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| @@ -0,0 +1,117 @@ +<tool id="retr_pepatlas1" name="Number of MS/MS observations in a tissue (from Peptide Atlas)" version="2018.08.22"> + <description> + </description> + <requirements> + <requirement type="package" version="3.4.1">R</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="Rscript"> + $__tool_directory__/proteore_ms_observation_pepatlas.R + --input_type="$input.ids" + #if $input.ids == "list" + --input="$input.list" + #else + --input="$input.file" + --column_number="$input.ncol" + --header="$input.header" + #end if + --atlas="$atlas" + --output="$output" + </command> + + <inputs> + <conditional name="input" > + <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > + <option value="list">Copy/paste your identifiers</option> + <option value="file" selected="true">Input file containing your identifiers</option> + </param> + <when value="list" > + <param name="list" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of Uniprot IDs" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <param name="ncol" type="text" value="c1" label="The column number of Uniprot IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + <!-- Peptide Atlas options --> + <param name="atlas" type="select" display="checkboxes" multiple="true" label="Please select proteomics dataset (sample)"> + <options from_data_table="peptide_atlas"> + <filter type="sort_by" column="2"/> + </options> + </param> + </inputs> + + <outputs> + <data name="output" format="tabular" label=""/> + </outputs> + + <tests> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="FKW_Lacombe_et_al_2017_OK.txt"/> + <param name="ncol" value="c1"/> + <param name="header" value="true"/> + </conditional> + + <!--${__HERE__} does not work here, you must put absolute path here and in test-data/peptide_atlas.loc --> + <param name="atlas" value="${__HERE__}/test-data/Human_Brain_18-07-2018.tsv"/> + + <output name="output" file="PeptideAtlas_output.txt"/> + </test> + </tests> + + <help><![CDATA[ + +Given a list of Uniprot accession number this tool indicates the number of times a protein +has(ve) been observed in a given sample using LC-MS/MS proteomics approach. +Could be of interest for people who wants to know to what extent a protein +is detectable (and to roughly estimate its level) in a given sample using proteomics. +Available human biological samples are the following: brain, heart, kidney, +liver, plasma, urine and cerebrospinal fluid (CSF). Data were retrieved from +Peptide Atlas release (Jan 2018). + +**Input required** + +A list of Uniprot accession number (e.g. Q12860) provided either in the form of +a file (if you choose a file, it is necessary to specify the column where +are your Uniprot accession number) or in a copy/paste mode. If your input file +or list contains other type of IDs, please use the ID_Converter tool to convert +yours into Uniprot accession number. + +**Output** + +Additional columns are created for each selected proteomics sample reporting +the number of times all peptides corresponding to a protein have been observed by +LC-MS/MS according to Peptide Atlas. “NA” means that no information has been reported +suggesting that this protein has not been observed in the sample of interest. + +---- + +**Authors** + +T.P. Lien Nguyen, David Christiany, 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 + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + ]]></help> + <citations> + </citations> +</tool> + |
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| diff -r 000000000000 -r 97e4d3a43537 test-data/FKW_Lacombe_et_al_2017_OK.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FKW_Lacombe_et_al_2017_OK.txt Wed Sep 19 05:16:37 2018 -0400 |
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| @@ -0,0 +1,154 @@ +Protein accession number (UniProt) Protein name Number of peptides (razor + unique) + +P15924 Desmoplakin 69 +P02538 Keratin, type II cytoskeletal 6A 53 +P02768 Serum albumin 44 +P08779 Keratin, type I cytoskeletal 16 29 +Q02413 Desmoglein-1 24 +P07355 "Annexin A2;Putative annexin A2-like protein" 22 +P14923 Junction plakoglobin 22 +P02788 Lactotransferrin 21 +Q9HC84 Mucin-5B 21 +P29508 Serpin B3 20 +P63261 Actin, cytoplasmic 2 19 +Q8N1N4 Keratin, type II cytoskeletal 78 18 +Q04695 Keratin, type I cytoskeletal 17 18 +P01876 Ig alpha-1 chain C region 16 +Q01469 Fatty acid-binding protein 5, epidermal 15 +P31944 Caspase-14 15 +P01833 Polymeric immunoglobulin receptor 15 +P06733 Alpha-enolase 15 +P25311 Zinc-alpha-2-glycoprotein 15 +Q15149 Plectin 15 +P19013 Keratin, type II cytoskeletal 4 13 +Q6KB66 Keratin, type II cytoskeletal 80 13 +Q08188 Protein-glutamine gamma-glutamyltransferase E 12 +P13646 Keratin, type I cytoskeletal 13 11 +Q86YZ3 Hornerin 11 +P04259 Keratin, type II cytoskeletal 6B 10 +P02545 "Prelamin-A/C;Lamin-A/C" 10 +P04083 Annexin A1 10 +P11021 78 kDa glucose-regulated protein 10 +P02787 Serotransferrin 9 +P04040 Catalase 9 +P31151 Protein S100-A7 9 +P31947 14-3-3 protein sigma 9 +Q96P63 Serpin B12 9 +P14618 Pyruvate kinase PKM 9 +P60174 Triosephosphate isomerase 9 +Q06830 Peroxiredoxin-1 9 +P01040 Cystatin-A 8 +P05089 Arginase-1 8 +P01834 Ig kappa chain C region 8 +P04406 Glyceraldehyde-3-phosphate dehydrogenase 8 +P0DMV9 Heat shock 70 kDa protein 1B 8 +P13639 Elongation factor 2 8 +P35579 Myosin-9 8 +P68371 Tubulin beta-4B chain 8 +Q8WVV4 Protein POF1B 8 +O75635 Serpin B7 7 +P01857 Ig gamma-1 chain C region 7 +P61626 Lysozyme C 7 +P68363 Tubulin alpha-1B chain 7 +P01009 "Alpha-1-antitrypsin;Short peptide from AAT" 6 +P07900 Heat shock protein HSP 90-alpha 6 +Q9NZH8 Interleukin-36 gamma 6 +O43707 "Alpha-actinin-4;Alpha-actinin-1" 6 +O75223 Gamma-glutamylcyclotransferase 6 +P00338 L-lactate dehydrogenase A chain 6 +P07339 Cathepsin D 6 +P62987 Ubiquitin-60S ribosomal protein L40 6 +P10599 Thioredoxin 6 +Q9UGM3 Deleted in malignant brain tumors 1 protein 6 +Q9UI42 Carboxypeptidase A4 6 +P47929 Galectin-7 5 +Q13867 Bleomycin hydrolase 5 +Q6P4A8 Phospholipase B-like 1 5 +O75369 Filamin-B 5 +P00441 Superoxide dismutase [Cu-Zn] 5 +P04792 Heat shock protein beta-1 5 +P11142 Heat shock cognate 71 kDa protein 5 +P58107 Epiplakin 5 +P60842 Eukaryotic initiation factor 4A-I 5 +P62937 Peptidyl-prolyl cis-trans isomerase A 5 +P63104 14-3-3 protein zeta/delta 5 +Q92820 Gamma-glutamyl hydrolase 5 +O75342 Arachidonate 12-lipoxygenase, 12R-type 4 +P09211 Glutathione S-transferase P 4 +P31025 Lipocalin-1 4 +P48594 Serpin B4 4 +Q14574 Desmocollin-3 4 +Q5T750 Skin-specific protein 32 4 +Q6UWP8 Suprabasin 4 +O60911 Cathepsin L2 4 +P00558 Phosphoglycerate kinase 1 4 +P04075 Fructose-bisphosphate aldolase A 4 +P07384 Calpain-1 catalytic subunit 4 +P0CG05 Ig lambda-2 chain C regions 4 +P18206 Vinculin 4 +P62258 14-3-3 protein epsilon 4 +P68871 Hemoglobin subunit beta 4 +Q9C075 Keratin, type I cytoskeletal 23 4 +A8K2U0 Alpha-2-macroglobulin-like protein 1 3 +P00738 Haptoglobin 3 +P01011 Alpha-1-antichymotrypsin 3 +P02763 Alpha-1-acid glycoprotein 1 3 +P18510 Interleukin-1 receptor antagonist protein 3 +P22528 Cornifin-B 3 +P30740 Leukocyte elastase inhibitor 3 +P80188 Neutrophil gelatinase-associated lipocalin 3 +Q15828 Cystatin-M 3 +Q9HCY8 Protein S100-A14 3 +P01623 Ig kappa chain V-III region 3 +P01877 Ig alpha-2 chain C region 3 +P06396 Gelsolin 3 +P14735 Insulin-degrading enzyme 3 +P20933 N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase 3 +P25788 Proteasome subunit alpha type-3 3 +P26641 Elongation factor 1-gamma 3 +P36952 Serpin B5 3 +P40926 Malate dehydrogenase, mitochondrial 3 +Q9Y6R7 IgGFc-binding protein 3 +O95274 Ly6/PLAUR domain-containing protein 3 2 +P00491 Purine nucleoside phosphorylase 2 +P04080 Cystatin-B 2 +P09972 Fructose-bisphosphate aldolase C 2 +P19012 Keratin, type I cytoskeletal 15 2 +P20930 Filaggrin 2 +Q96FX8 p53 apoptosis effector related to PMP-22 2 +Q9UIV8 Serpin B13 2 +P01625 Ig kappa chain V-IV region Len 2 +P01765 Ig heavy chain V-III region TIL 2 +P01766 Ig heavy chain V-III region BRO 2 +P01860 Ig gamma-3 chain C region 2 +P01871 Ig mu chain C region 2 +P05090 Apolipoprotein D 2 +P06870 Kallikrein-1 2 +P07858 Cathepsin B 2 +P08865 40S ribosomal protein SA 2 +P11279 Lysosome-associated membrane glycoprotein 1 2 +P13473 Lysosome-associated membrane glycoprotein 2 2 +P19971 Thymidine phosphorylase 2 +P23284 Peptidyl-prolyl cis-trans isomerase B 2 +P23396 40S ribosomal protein S3 2 +P25705 ATP synthase subunit alpha, mitochondrial 2 +P27482 Calmodulin-like protein 3 2 +P31949 Protein S100-A11 2 +P40121 Macrophage-capping protein 2 +P42357 Histidine ammonia-lyase 2 +P47756 F-actin-capping protein subunit beta 2 +P48637 Glutathione synthetase 2 +P49720 Proteasome subunit beta type-3 2 +P50395 Rab GDP dissociation inhibitor beta 2 +P59998 Actin-related protein 2/3 complex subunit 4 2 +P61160 Actin-related protein 2 2 +P61916 Epididymal secretory protein E1 2 +P04745 Alpha-amylase 1 23 +Q9NZT1 Calmodulin-like protein 5 8 +P12273 Prolactin-inducible protein 6 +Q96DA0 Zymogen granule protein 16 homolog B 5 +P01036 Cystatin-S 5 +Q8TAX7 Mucin-7 2 +P01037 Cystatin-SN 2 +P09228 Cystatin-SA 2 + |
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| diff -r 000000000000 -r 97e4d3a43537 test-data/Human_Brain_25-07-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Human_Brain_25-07-2018.tsv Wed Sep 19 05:16:37 2018 -0400 |
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| b'@@ -0,0 +1,82387 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|
| b |
| diff -r 000000000000 -r 97e4d3a43537 test-data/Human_CSF_25-07-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Human_CSF_25-07-2018.tsv Wed Sep 19 05:16:37 2018 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r 97e4d3a43537 test-data/Human_Heart_25-07-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Human_Heart_25-07-2018.tsv Wed Sep 19 05:16:37 2018 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r 97e4d3a43537 test-data/Human_Kidney_25-07-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Human_Kidney_25-07-2018.tsv Wed Sep 19 05:16:37 2018 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r 97e4d3a43537 test-data/Human_Liver_25-07-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Human_Liver_25-07-2018.tsv Wed Sep 19 05:16:37 2018 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r 97e4d3a43537 test-data/Human_Plasma_25-07-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Human_Plasma_25-07-2018.tsv Wed Sep 19 05:16:37 2018 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r 97e4d3a43537 test-data/Human_Urine_25-07-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Human_Urine_25-07-2018.tsv Wed Sep 19 05:16:37 2018 -0400 |
| b |
| b'@@ -0,0 +1,80172 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|
| b |
| diff -r 000000000000 -r 97e4d3a43537 test-data/PeptideAtlas_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PeptideAtlas_output.txt Wed Sep 19 05:16:37 2018 -0400 |
| b |
| b'@@ -0,0 +1,152 @@\n+Protein accession number (UniProt)\tProtein name\tNumber of peptides (razor + unique)\tHuman_Liver_25-07-2018\tHuman_Brain_25-07-2018\tHuman_Heart_25-07-2018\tHuman_Kidney_25-07-2018\tHuman_CSF_25-07-2018\tHuman_Plasma_25-07-2018\tHuman_Urine_25-07-2018\n+P15924\tDesmoplakin\t69\t142377\t95096\t168528\t77390\t85770\t119354\t138592\n+P02538\tKeratin, type II cytoskeletal 6A\t53\t319974\t328169\t303239\t324409\t319406\t329783\t321966\n+P02768\tSerum albumin\t44\t4034248\t4061388\t3987900\t4014664\t4128717\t4101660\t4147099\n+P08779\tKeratin, type I cytoskeletal 16\t29\t211637\t226951\t212075\t220729\t213732\t222534\t235473\n+Q02413\tDesmoglein-1\t24\t8028\t11289\t7420\t7895\t16628\t13979\t13369\n+P07355\t"Annexin A2;Putative annexin A2-like protein"\t22\t335937\t329192\t336660\t340540\t217766\t325970\t337207\n+P14923\tJunction plakoglobin\t22\t63373\t58265\t69043\t52170\t47245\t56259\t62907\n+P02788\tLactotransferrin\t21\t125966\t129200\t65470\t121362\t122529\t124893\t133482\n+Q9HC84\tMucin-5B\t21\tNA\tNA\t513\tNA\t622\t3125\t7020\n+P29508\tSerpin B3\t20\t4825\t7614\t4825\t5027\t5655\t14510\t11231\n+P63261\tActin, cytoplasmic 2\t19\t2507222\t2539480\t2451756\t2507619\t2154824\t2337394\t2527283\n+Q8N1N4\tKeratin, type II cytoskeletal 78\t18\t30583\t33292\t26078\t31009\t30980\t30402\t29408\n+Q04695\tKeratin, type I cytoskeletal 17\t18\t115279\t164532\t140917\t134017\t150620\t143360\t164560\n+P01876\tIg alpha-1 chain C region\t16\t757578\t730284\t705165\t740554\t783544\t793560\t817430\n+Q01469\tFatty acid-binding protein 5, epidermal\t15\t39479\t39522\t42540\t35783\t35719\t38758\t37129\n+P31944\tCaspase-14\t15\tNA\t1391\t1137\tNA\t2533\t4624\t2880\n+P01833\tPolymeric immunoglobulin receptor\t15\t20841\t7248\tNA\t50469\t30073\t58502\t53354\n+P06733\tAlpha-enolase\t15\t823360\t830567\t822618\t833016\t780302\t788901\t814010\n+P25311\tZinc-alpha-2-glycoprotein\t15\t537210\t534097\t354079\t535898\t583956\t601524\t585402\n+Q15149\tPlectin\t15\t555953\t518832\t611842\t606213\t1648\t28513\t492273\n+P19013\tKeratin, type II cytoskeletal 4\t13\t76328\t74580\t72973\t83227\t73803\t79318\t73240\n+Q6KB66\tKeratin, type II cytoskeletal 80\t13\t48823\t44759\t49924\t48632\t44976\t46104\t47250\n+Q08188\tProtein-glutamine gamma-glutamyltransferase E\t12\tNA\t2107\tNA\t99\t2838\t2081\t3880\n+P13646\tKeratin, type I cytoskeletal 13\t11\t121760\t99000\t122818\t131912\t111069\t134774\t129736\n+Q86YZ3\tHornerin\t11\t15140\t35518\t42208\t38988\t38668\t37872\t36925\n+P04259\tKeratin, type II cytoskeletal 6B\t10\t347317\t363626\t332829\t352955\t356419\t360519\t356657\n+P02545\t"Prelamin-A/C;Lamin-A/C"\t10\t275428\t264913\t276787\t275488\tNA\t162486\t259543\n+P04083\tAnnexin A1\t10\t165351\t160085\t168636\t164137\t47845\t166007\t163612\n+P11021\t78 kDa glucose-regulated protein\t10\t491857\t474661\t475436\t481012\t437635\t399700\t490259\n+P02787\tSerotransferrin\t9\t865282\t879183\t856893\t877445\t923227\t894492\t919022\n+P04040\tCatalase\t9\t102248\t93889\t94113\t99426\t63719\t66687\t98376\n+P31151\tProtein S100-A7\t9\tNA\t6885\tNA\t2009\t6353\t9825\t8737\n+P31947\t14-3-3 protein sigma\t9\t91984\t79919\t80042\t73306\t68316\t86007\t94351\n+Q96P63\tSerpin B12\t9\t809\t620\t487\t1296\t2160\t1967\t1179\n+P14618\tPyruvate kinase PKM\t9\t689710\t720750\t708696\t704253\t684744\t640757\t711201\n+P60174\tTriosephosphate isomerase\t9\t301704\t303161\t300425\t302164\t284053\t284248\t298321\n+Q06830\tPeroxiredoxin-1\t9\t228019\t228763\t226445\t225920\t205221\t197577\t224285\n+P01040\tCystatin-A\t8\t6904\t4253\tNA\t1794\t7036\t7016\t5230\n+P05089\tArginase-1\t8\t12530\t2871\t3482\t10293\t6068\t7653\t8927\n+P01834\tIg kappa chain C region\t8\t903130\t942720\t906883\t925001\t948102\t964189\t966351\n+P04406\tGlyceraldehyde-3-phosphate dehydrogenase\t8\t1077059\t1094095\t1070354\t1068230\t906215\t940688\t1071397\n+P0DMV9\tHeat shock 70 kDa protein 1B\t8\t429972\t436937\t434045\t429652\t259144\t345698\t422131\n+P13639\tElongation factor 2\t8\t495316\t486368\t474412\t438027\t206888\t271655\t474649\n+P35579\tMyosin-9\t8\t1268893\t1225860\t1226696\t1263466\t201637\t739201\t1247876\n+P68371\tTubulin beta-4B chain\t8\t990617\t1021213\t986037\t992796\t790075\t912254\t991679\n+Q8WVV4\tProtein POF1B\t8\tNA\tNA\t1052\tNA\tNA\t611\t1968\n+O75635\tSerpin B7\t7\tNA\tNA\t347\tNA\t79\tNA\t25\n+P01857\tIg gamma-1 chain C region\t7\t1050908\t1067267\t1008293\t1045235\t1102986\t1095909\t1108030\n+P61626\tLysozyme C\t7\t49818\t38215\t43160\t51886\t52883\t52355\t5'..b'58\t18312\t19725\t21516\t21452\n+Q15828\tCystatin-M\t3\tNA\tNA\tNA\tNA\t3599\t3987\t3480\n+Q9HCY8\tProtein S100-A14\t3\t2821\tNA\t1082\tNA\tNA\t2165\t2134\n+P01623\tIg kappa chain V-III region\t3\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01877\tIg alpha-2 chain C region\t3\t694555\t716305\t700857\t723856\t730305\t747506\t768606\n+P06396\tGelsolin\t3\t1287447\t1379383\t1274407\t1302527\t1419817\t1169333\t1337014\n+P14735\tInsulin-degrading enzyme\t3\t17861\t13629\t12516\t13372\tNA\tNA\t14521\n+P20933\tN(4)-(beta-N-acetylglucosaminyl)-L-asparaginase\t3\t3008\t2805\t1266\t2780\t4014\t2979\t3418\n+P25788\tProteasome subunit alpha type-3\t3\t35950\t36236\t36013\t36371\t3575\t11062\t36074\n+P26641\tElongation factor 1-gamma\t3\t137404\t136298\t134511\t137325\t31309\t49630\t133526\n+P36952\tSerpin B5\t3\t2256\t623\t2598\tNA\t3128\t6451\t10291\n+P40926\tMalate dehydrogenase, mitochondrial\t3\t218645\t221494\t217935\t213830\t191296\t185563\t212686\n+Q9Y6R7\tIgGFc-binding protein\t3\t1278\t18889\tNA\tNA\t46380\t35431\t25645\n+O95274\tLy6/PLAUR domain-containing protein 3\t2\t303\tNA\t303\t303\tNA\t970\t669\n+P00491\tPurine nucleoside phosphorylase\t2\t73794\t74481\t60134\t75554\t11054\t69633\t70355\n+P04080\tCystatin-B\t2\t37617\t37392\t35821\t35086\t33109\t34957\t35223\n+P09972\tFructose-bisphosphate aldolase C\t2\t105683\t110996\t111021\t101042\t105270\t82178\t106823\n+P19012\tKeratin, type I cytoskeletal 15\t2\t110524\t90350\t112120\t113472\t98435\t115279\t114900\n+P20930\tFilaggrin\t2\t808\t617\t1566\t574\t2386\t2376\t1111\n+Q96FX8\tp53 apoptosis effector related to PMP-22\t2\tNA\tNA\t184\tNA\t149\t166\tNA\n+Q9UIV8\tSerpin B13\t2\tNA\tNA\tNA\tNA\tNA\t452\t83\n+P01625\tIg kappa chain V-IV region Len\t2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01765\tIg heavy chain V-III region TIL\t2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01766\tIg heavy chain V-III region BRO\t2\t111574\t119483\t114044\t117768\t117860\t115780\t123431\n+P01860\tIg gamma-3 chain C region\t2\t460682\t473345\t440313\t481015\t501453\t485795\t496332\n+P01871\tIg mu chain C region\t2\t736466\t764638\t657382\t786819\t836997\t798608\t928187\n+P05090\tApolipoprotein D\t2\t488723\t505850\t341408\t508056\t524003\t528820\t524688\n+P06870\tKallikrein-1\t2\tNA\tNA\tNA\tNA\tNA\t1625\t1024\n+P07858\tCathepsin B\t2\t47127\t45065\t46514\t46312\t48159\t47773\t42954\n+P08865\t40S ribosomal protein SA\t2\t99729\t97595\t96640\t96167\t51713\t52101\t96976\n+P11279\tLysosome-associated membrane glycoprotein 1\t2\t24913\t24679\t24062\t24264\t25469\t26241\t25579\n+P13473\tLysosome-associated membrane glycoprotein 2\t2\t23679\t23514\t18416\t19052\t24363\t21031\t24678\n+P19971\tThymidine phosphorylase\t2\t32407\t19710\t25649\t31407\t3388\t5945\t21690\n+P23284\tPeptidyl-prolyl cis-trans isomerase B\t2\t119688\t114725\t119112\t112433\t100047\t108025\t109113\n+P23396\t40S ribosomal protein S3\t2\t137018\t136944\t135917\t135012\t32039\t72562\t136725\n+P25705\tATP synthase subunit alpha, mitochondrial\t2\t324452\t326832\t327400\t320630\t166214\t256636\t311414\n+P27482\tCalmodulin-like protein 3\t2\t7456\t7195\t7871\t8480\t7456\t7995\t9163\n+P31949\tProtein S100-A11\t2\t55429\t49274\t55429\t56325\t45021\t54436\t56222\n+P40121\tMacrophage-capping protein\t2\t43287\t43160\t33903\t47582\t40785\t41526\t42788\n+P42357\tHistidine ammonia-lyase\t2\t1319\tNA\tNA\tNA\tNA\t194\t773\n+P47756\tF-actin-capping protein subunit beta\t2\t74271\t73745\t74628\t73510\t15808\t43027\t72866\n+P48637\tGlutathione synthetase\t2\t20159\t18744\t18632\t21873\t14923\t3818\t16190\n+P49720\tProteasome subunit beta type-3\t2\t31654\t32439\t32155\t32573\t13487\t13395\t32246\n+P50395\tRab GDP dissociation inhibitor beta\t2\t175982\t175993\t171306\t171156\t154570\t146606\t169222\n+P59998\tActin-related protein 2/3 complex subunit 4\t2\t32136\t32013\t32332\t32426\t26318\t20742\t32640\n+P61160\tActin-related protein 2\t2\t77943\t78449\t77224\t78687\t15307\t39910\t77033\n+P61916\tEpididymal secretory protein E1\t2\t17480\t16620\t16488\t18374\t19741\t17549\t16996\n+P04745\tAlpha-amylase 1\t23\tNA\t5263\tNA\tNA\t12036\t18282\t16843\n+Q9NZT1\tCalmodulin-like protein 5\t8\t4805\t5432\t7591\t5503\t4570\t6450\t8086\n+P12273\tProlactin-inducible protein\t6\t6814\t8960\t3797\t11248\t13545\t18727\t20201\n+Q96DA0\tZymogen granule protein 16 homolog B\t5\tNA\tNA\tNA\tNA\t1560\t3455\t2700\n+P01036\tCystatin-S\t5\tNA\tNA\tNA\tNA\t2577\t5348\t8225\n+Q8TAX7\tMucin-7\t2\tNA\tNA\tNA\tNA\t25\tNA\t339\n+P01037\tCystatin-SN\t2\tNA\tNA\tNA\tNA\t3437\t5086\t8969\n+P09228\tCystatin-SA\t2\tNA\tNA\tNA\tNA\t491\t3406\t3264\n' |
| b |
| diff -r 000000000000 -r 97e4d3a43537 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Sep 19 05:16:37 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ + +<tables> + <!-- Location of peptide reference files for proteore_ms_observation --> + <table name='peptide_atlas' comment_char="#"> + <columns>tissue,name,value</columns> + <file path="tool-data/peptide_atlas.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 97e4d3a43537 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Sep 19 05:16:37 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of peptide reference files for proteore_ms_observation --> + <table name='peptide_atlas' comment_char="#"> + <columns>tissue,name,value</columns> + <file path="/home/dchristiany/proteore_project/ProteoRE/tools/retrieve_msbased_pepatlas/test-data/peptide_atlas.loc" /> + </table> +</tables> |