From ce5091351459c8b30fc32674097503b13777e0a8 Mon Sep 17 00:00:00 2001 From: Enrique Date: Wed, 22 Mar 2017 12:35:46 +0000 Subject: [PATCH 1/3] counter added --- QC_Export_MGF/Counter_files.py | 188 +++++++++++++++++++++++++++++++++ 1 file changed, 188 insertions(+) create mode 100755 QC_Export_MGF/Counter_files.py diff --git a/QC_Export_MGF/Counter_files.py b/QC_Export_MGF/Counter_files.py new file mode 100755 index 0000000..67c605f --- /dev/null +++ b/QC_Export_MGF/Counter_files.py @@ -0,0 +1,188 @@ +#This program takes different information from .MGF files in order to generate different outputs that will be used by the R Script. + +# IMPORTANT INFORMATION. In the release of 2014, we didn't used any filter previusly, because of that we'll not have two folders (Identify and +# unidentify files). For futures releases (Ex. 2017 and 2018, ), remove the # from PATH_RELEASE_UNID and remove None. +#Remember to change the PATH with the new release in future QCs. +import glob +import os + +def file_checker(): + ################################################################ + """The PATH of these function must be changed in each release""" + PATH_RELEASE1_IDEN = os.getcwd()+'/archive_all_2014-10/' + PATH_RELEASE1_UNIDE = None + #PATH_RELEASE1_UNIDE = os.getcwd()+'/archive_all_2014-10/' + + PATH_RELEASE2_IDEN = os.getcwd()+'/archive_all_2016-10/archive_identified_2016-10/' + PATH_RELEASE2_UNIDE = os.getcwd() + '/archive_all_2016-10/archive_unidentified_2016-10/' + ################################################################ + + #This global function finds the .mgf files + list_of_files_release1_ide = glob.glob(PATH_RELEASE1_IDEN+'*.mgf') + list_of_files_release1_unide = None #REMOVE THIS PART AND UNCOMMENT NEXT LINE IN NEXT RELEASES. + + #list_of_files_release1_unid = glob.glob(PATH_RELEASE1_UNID'+*.mgf') + + list_of_files_release2_ide = glob.glob(PATH_RELEASE2_IDEN+'*.mgf') + list_of_files_release2_unide = glob.glob(PATH_RELEASE2_UNIDE+'*.mgf') + + #Check if exist cache folder. If not will make it. + #RELEASE 1 + if not os.path.exists(PATH_RELEASE1_IDEN+'cache'): + os.makedirs(PATH_RELEASE1_IDEN+'cache') + + # if not os.path.exists(PATH_RELEASE1_UNIDE'+cache'): + # os.makedirs(PATH_RELEASE1_UNIDE'+cache') + + #RELEASE2 + if not os.path.exists(PATH_RELEASE2_IDEN+'cache'): + os.makedirs(PATH_RELEASE2_IDEN+'cache') + + if not os.path.exists(PATH_RELEASE2_UNIDE+'cache'): + os.makedirs(PATH_RELEASE2_UNIDE+'cache') + + + return PATH_RELEASE1_IDEN, \ + PATH_RELEASE2_IDEN, \ + PATH_RELEASE2_UNIDE, \ + list_of_files_release1_ide, \ + list_of_files_release2_ide, \ + list_of_files_release2_unide + + + +def read_files(list_of_files, path): + results = {True:[], False:[]} + + for fileName in list_of_files: + + with open(fileName) as fp: + register = {} + identified = False + for line in fp: + line = line.rstrip() + if (line.find('TITLE') != -1 or line.find('PEPMASS') != -1 or line.find('CHARGE') != -1 or line.find('SEQ') != -1 or line.find('USER03') != -1 or line.find('TAXONOMY') != -1): + if(line.find('TITLE=id')!=-1): + parts = line.split(';') + elements = parts[0].split('=') + spectrum = parts[2].split('=') + composition = {} + composition['id'] = elements[2] + composition['file'] = parts[1] + composition['spectrum'] = spectrum[1] + + register[elements[0]] = composition + else: + elements = line.split('=') + register[elements[0]] = elements[1] + if(line.find('SEQ') != -1): + identified = True + elif (line.find('END IONS') != -1): + results[identified].append(register) + identified = False + register = {} + + # for result in results: + # if result: + # print('identified') + # else: + # print('DESidentified') + # for register in results[result]: + # print(" > ID: "+register['TITLE']['id']) + # print(" > Spectrum: "+register['TITLE']['spectrum']) + # print(" > XML: "+register['TITLE']['file']) + # if(result): + # print(" > SEQ: "+register['SEQ']) + # print(" > USER:"+register['USER03']) + # print(" > TAXONOMY:"+register['TAXONOMY']) + # print('') + + # + # print('TOTAL OF REGISTERS') + # print('IDENTIFY : '+str(len(results[True]))+" registers") + # print('UNIDENTIFY : '+str(len(results[False]))+" registers") + +#METER UN IF COMO EN EL ANTERIOR CASO PARA QUE TE IMPRIMA AQUELLOS QUE SON FALSOS Y LOS QUE SON VERDADEROS. + + for result in results: + if result: + if len(results[True]) != 0: + with open(os.path.join(path+'ID_identify.txt'), 'w') as output: + for register in results[result]: + output.write(register['TITLE']['id']+"\n") + output.close() + + with open(os.path.join(path+'spectrum_identify.txt'), 'w') as output: + for register in results[result]: + output.write(register['TITLE']['spectrum']+"\n") + output.close() + + with open(os.path.join(path + 'taxonomy_identify.txt'), 'w') as output: + for register in results[result]: + output.write(register['TAXONOMY'] + "\n") + output.close() + + if (result): + with open(os.path.join(path+'SEQ.txt'), 'w') as output: + for register in results[result]: + output.write(register['SEQ']+"\n") + output.close() + + with open(os.path.join(path+'USER03.txt'), 'w') as output: + for register in results[result]: + output.write(register['USER03']+"\n") + output.close() + else: + if len(results[False])!=0: + with open(os.path.join(path+'ID_unidentify.txt'), 'w') as output: + for register in results[result]: + output.write(register['TITLE']['id']+"\n") + output.close() + + with open(os.path.join(path+'spectrum_unidentify.txt'), 'w') as output: + for register in results[result]: + output.write(register['TITLE']['spectrum']+"\n") + output.close() + + with open(os.path.join(path + 'taxonomy_unidentify.txt'), 'w') as output: + for register in results[result]: + output.write(register['TAXONOMY'] + "\n") + output.close() + + if (result): + with open(os.path.join(path+'SEQ.txt'), 'w') as output: + for register in results[result]: + output.write(register['SEQ']+"\n") + output.close() + + with open(os.path.join(path+'USER03.txt'), 'w') as output: + for register in results[result]: + output.write(register['USER03']+"\n") + output.close() + + + +def main(): + + + (PATH_RELEASE1_IDEN, + PATH_RELEASE2_IDEN, + PATH_RELEASE2_UNIDE, + list_of_files_release1_ide, + list_of_files_release2_ide, + list_of_files_release2_unide) = file_checker() + + read_files(list_of_files_release1_ide, PATH_RELEASE1_IDEN+'cache/') + + #read_files(list_of_files_release1_unide, PATH_RELEASE1_+'cache/') + + read_files(list_of_files_release2_ide, PATH_RELEASE2_IDEN+'cache/') + + read_files(list_of_files_release2_unide, PATH_RELEASE2_UNIDE+'cache/') + + + + + +if __name__ == "__main__": + main() \ No newline at end of file From fe0c1ebdcb8d0656f4ba44c469f011d9b999022c Mon Sep 17 00:00:00 2001 From: Enrique Date: Fri, 31 Mar 2017 11:06:11 +0100 Subject: [PATCH 2/3] New release of the MGF files and improved documentations --- QC_Export_MGF/Counter_files.py | 228 +- QC_Export_MGF/Identify_detector.pl | 27 - QC_Export_MGF/QC_MGF_test.Rmd | 477 ++ QC_Export_MGF/QC_MGF_test.html | 318 + QC_Export_MGF/QC_exporter_run.sh | 20 + QC_Export_MGF/Script_QC_MGF.R | 276 - QC_Export_MGF/Script_QC_MGF.Rmd | 378 - QC_Export_MGF/Script_QC_MGF.html | 12302 --------------------------- QC_Export_MGF/counter.py | 39 - README.md | 36 +- 10 files changed, 1004 insertions(+), 13097 deletions(-) delete mode 100644 QC_Export_MGF/Identify_detector.pl create mode 100644 QC_Export_MGF/QC_MGF_test.Rmd create mode 100644 QC_Export_MGF/QC_MGF_test.html create mode 100644 QC_Export_MGF/QC_exporter_run.sh delete mode 100644 QC_Export_MGF/Script_QC_MGF.R delete mode 100644 QC_Export_MGF/Script_QC_MGF.Rmd delete mode 100644 QC_Export_MGF/Script_QC_MGF.html delete mode 100644 QC_Export_MGF/counter.py diff --git a/QC_Export_MGF/Counter_files.py b/QC_Export_MGF/Counter_files.py index 67c605f..d9f5001 100755 --- a/QC_Export_MGF/Counter_files.py +++ b/QC_Export_MGF/Counter_files.py @@ -1,23 +1,30 @@ -#This program takes different information from .MGF files in order to generate different outputs that will be used by the R Script. -# IMPORTANT INFORMATION. In the release of 2014, we didn't used any filter previusly, because of that we'll not have two folders (Identify and -# unidentify files). For futures releases (Ex. 2017 and 2018, ), remove the # from PATH_RELEASE_UNID and remove None. -#Remember to change the PATH with the new release in future QCs. +"""This program takes different information from .MGF files in order to generate different outputs that will be used by the R Script. +IMPORTANT INFORMATION. In the release of 2014, we didn't used any filter previusly, because of that we'll not have two folders (Identify and +unidentify files). For futures releases (Ex. 2017 and 2018, ), remove the # from PATH_RELEASE_UNID and remove the line: PATH_RELEASE1_UNIDE = None + +Remember to change the PATH with the new release in future QCs and uncomment the function in main() in order to compare futures releases with filters (Ex. 2017 and 2018)""" + + import glob -import os +import os +import re +from collections import Counter + def file_checker(): - ################################################################ """The PATH of these function must be changed in each release""" + PATH_RELEASE1_IDEN = os.getcwd()+'/archive_all_2014-10/' PATH_RELEASE1_UNIDE = None #PATH_RELEASE1_UNIDE = os.getcwd()+'/archive_all_2014-10/' PATH_RELEASE2_IDEN = os.getcwd()+'/archive_all_2016-10/archive_identified_2016-10/' PATH_RELEASE2_UNIDE = os.getcwd() + '/archive_all_2016-10/archive_unidentified_2016-10/' - ################################################################ - #This global function finds the .mgf files + + #From here don't change anything. + #This global function finds the .mgf files in paths list_of_files_release1_ide = glob.glob(PATH_RELEASE1_IDEN+'*.mgf') list_of_files_release1_unide = None #REMOVE THIS PART AND UNCOMMENT NEXT LINE IN NEXT RELEASES. @@ -26,6 +33,7 @@ def file_checker(): list_of_files_release2_ide = glob.glob(PATH_RELEASE2_IDEN+'*.mgf') list_of_files_release2_unide = glob.glob(PATH_RELEASE2_UNIDE+'*.mgf') + #Check if exist cache folder. If not will make it. #RELEASE 1 if not os.path.exists(PATH_RELEASE1_IDEN+'cache'): @@ -52,10 +60,12 @@ def file_checker(): def read_files(list_of_files, path): + + "This function creates a list in order to classificate different releases between identify and unidentify. This also create outputs with different information that will be used in the R script" results = {True:[], False:[]} for fileName in list_of_files: - + results = {True: [], False: []} with open(fileName) as fp: register = {} identified = False @@ -81,6 +91,85 @@ def read_files(list_of_files, path): results[identified].append(register) identified = False register = {} + fp.close() + + for result in results: + if result: + if len(results[True]) != 0: + with open(os.path.join(path + 'ID_identify.txt'), 'a') as output: + for register in results[result]: + output.write(register['TITLE']['id'] + "\n") + output.close() + + with open(os.path.join(path + 'spectrum_identify.txt'), 'a') as output: + for register in results[result]: + output.write(register['TITLE']['spectrum'] + "\n") + output.close() + + with open(os.path.join(path + 'taxonomy_identify.txt'), 'a') as output: + for register in results[result]: + if 'TAXONOMY' in register: + output.write(register['TAXONOMY'] + "\n") + else: + continue + output.close() + + if (result): + with open(os.path.join(path + 'SEQ.txt'), 'a') as output: + for register in results[result]: + output.write(register['SEQ'] + "\n") + output.close() + + with open(os.path.join(path + 'modifications.txt'), 'a') as output: + for register in results[result]: + if bool(re.match('MS:', register["USER03"])): + with open(path + 'MS_files.txt', 'a') as MS_file: + MS_file.write(register['USER03'] + "\n") + MS_file.close() + line1 = re.sub("MS:" + "\d+", "", register['USER03']) + line2 = line1.replace(";", ",").replace("\n", ",") + new_string = re.sub(',+', ',', line2) + new_string2 = new_string.replace(",", "\n") + new_string3 = re.sub('\d+\-', '', new_string2) + + if not new_string3.strip(): + continue + if new_string3: + output.write(new_string3 + "\n") + output.close() + + + else: + if len(results[False]) != 0: + with open(os.path.join(path + 'ID_unidentify.txt'), 'a') as output: + for register in results[result]: + output.write(register['TITLE']['id'] + "\n") + output.close() + + with open(os.path.join(path + 'spectrum_unidentify.txt'), 'a') as output: + for register in results[result]: + output.write(register['TITLE']['spectrum'] + "\n") + output.close() + + + with open(os.path.join(path + 'taxonomy_unidentify.txt'), 'a') as output: + for register in results[result]: + if 'TAXONOMY' in register: + output.write(register['TAXONOMY'] + "\n") + else: + continue + output.close() + + # if (result): + # with open(os.path.join(path + 'SEQ.txt'), 'a') as output: + # for register in results[result]: + # output.write(register['SEQ'] + "\n") + # output.close() + # + # with open(os.path.join(path + 'modifications.txt'), 'a') as output: + # for register in results[result]: + # output.write(register['USER03'] + "\n") + # output.close() # for result in results: # if result: @@ -102,69 +191,75 @@ def read_files(list_of_files, path): # print('IDENTIFY : '+str(len(results[True]))+" registers") # print('UNIDENTIFY : '+str(len(results[False]))+" registers") -#METER UN IF COMO EN EL ANTERIOR CASO PARA QUE TE IMPRIMA AQUELLOS QUE SON FALSOS Y LOS QUE SON VERDADEROS. +#"""This part creates the output files""" - for result in results: - if result: - if len(results[True]) != 0: - with open(os.path.join(path+'ID_identify.txt'), 'w') as output: - for register in results[result]: - output.write(register['TITLE']['id']+"\n") - output.close() - with open(os.path.join(path+'spectrum_identify.txt'), 'w') as output: - for register in results[result]: - output.write(register['TITLE']['spectrum']+"\n") - output.close() - with open(os.path.join(path + 'taxonomy_identify.txt'), 'w') as output: - for register in results[result]: - output.write(register['TAXONOMY'] + "\n") - output.close() +def column_creator(path): - if (result): - with open(os.path.join(path+'SEQ.txt'), 'w') as output: - for register in results[result]: - output.write(register['SEQ']+"\n") - output.close() + """This function creates a table with the frequency of each element""" + if not os.path.exists(path+'tables'): + os.makedirs(path+'tables') - with open(os.path.join(path+'USER03.txt'), 'w') as output: - for register in results[result]: - output.write(register['USER03']+"\n") - output.close() - else: - if len(results[False])!=0: - with open(os.path.join(path+'ID_unidentify.txt'), 'w') as output: - for register in results[result]: - output.write(register['TITLE']['id']+"\n") - output.close() - with open(os.path.join(path+'spectrum_unidentify.txt'), 'w') as output: - for register in results[result]: - output.write(register['TITLE']['spectrum']+"\n") - output.close() + # Sequences + if os.path.exists(path+'SEQ.txt'): + with open(os.path.join(path+'SEQ.txt')) as f1, open(os.path.join(path+'tables/sequences_table.txt'), 'a') as f2: + c = Counter(x.strip() for x in f1) + for x in c: + f2.write("%s\t%s\n" % (x, str(c[x]))) + f1.close() + f2.close() - with open(os.path.join(path + 'taxonomy_unidentify.txt'), 'w') as output: - for register in results[result]: - output.write(register['TAXONOMY'] + "\n") - output.close() + # Modifications + if os.path.exists(path + 'modifications.txt'): - if (result): - with open(os.path.join(path+'SEQ.txt'), 'w') as output: - for register in results[result]: - output.write(register['SEQ']+"\n") - output.close() + with open(os.path.join(path+'modifications.txt')) as f1, open(os.path.join(path+'tables/modifications_table.txt'), 'a') as f2: + c = Counter(x.strip() for x in f1) + for x in c: + f2.write("%s\t%s\n" % (x, str(c[x]))) + f1.close() + f2.close() - with open(os.path.join(path+'USER03.txt'), 'w') as output: - for register in results[result]: - output.write(register['USER03']+"\n") - output.close() + # Spectrum identify: + if os.path.exists(path + 'spectrum_identify.txt'): + + with open(os.path.join(path+'spectrum_identify.txt')) as f1, open(path+'tables/spectrum_ide_table.txt', 'a') as f3: + lines1 = f1.read().count('\n') + f3.write("%s\n%s\n" % ("Spectrum Number",lines1)) + f1.close() + f3.close() + if os.path.exists(path + 'spectrum_unidentify.txt'): + with open(os.path.join(path+'spectrum_unidentify.txt')) as f2, open(path+'tables/spectrum_unide_table.txt', 'a') as f3: + lines2 = f2.read().count('\n') + f3.write("%s\n%s\n" % ("Spectrum Number",lines2)) + f2.close() + f3.close() + if os.path.exists(path+'taxonomy_identify.txt'): + # Taxonomy ide: + with open(os.path.join(path+'taxonomy_identify.txt')) as f1, open(os.path.join(path+'tables/taxonomy_ide_table.txt'), 'a') as f2: + c = Counter(x.strip() for x in f1) + for x in c: + f2.write("%s\t%s\n" % (x, str(c[x]))) + f1.close() + f2.close() + + + if os.path.exists(path + 'taxonomy_unidentify.txt'): + # Taxonomy unide: + with open(os.path.join(path+'taxonomy_unidentify.txt')) as f1, open(os.path.join(path+'tables/taxonomy_unide_table.txt'), 'a') as f2: + c = Counter(x.strip() for x in f1) + for x in c: + f2.write("%s\t%s\n" % (x, str(c[x]))) + f1.close() + f2.close() def main(): +#Generate the path that we're going to use in the next function (PATH_RELEASE1_IDEN, PATH_RELEASE2_IDEN, PATH_RELEASE2_UNIDE, @@ -172,17 +267,18 @@ def main(): list_of_files_release2_ide, list_of_files_release2_unide) = file_checker() - read_files(list_of_files_release1_ide, PATH_RELEASE1_IDEN+'cache/') - - #read_files(list_of_files_release1_unide, PATH_RELEASE1_+'cache/') - - read_files(list_of_files_release2_ide, PATH_RELEASE2_IDEN+'cache/') - - read_files(list_of_files_release2_unide, PATH_RELEASE2_UNIDE+'cache/') - - +#Create main files. + read_files(list_of_files_release1_ide, PATH_RELEASE1_IDEN+'cache/') #RELEASE1_identify + #read_files(list_of_files_release1_unide, PATH_RELEASE1_+'cache/') #RELEASE1_unidentify + read_files(list_of_files_release2_ide, PATH_RELEASE2_IDEN+'cache/') #RELEASE2_identify + read_files(list_of_files_release2_unide, PATH_RELEASE2_UNIDE+'cache/') #RELEASE2_unidentify +#Create frequency tables + column_creator(PATH_RELEASE1_IDEN+'cache/') + #column_creator(PATH_RELEASE1_IDEN + 'cache/') + column_creator(PATH_RELEASE2_IDEN + 'cache/') + column_creator(PATH_RELEASE2_UNIDE + 'cache/') if __name__ == "__main__": main() \ No newline at end of file diff --git a/QC_Export_MGF/Identify_detector.pl b/QC_Export_MGF/Identify_detector.pl deleted file mode 100644 index 76d5081..0000000 --- a/QC_Export_MGF/Identify_detector.pl +++ /dev/null @@ -1,27 +0,0 @@ - - -use strict; -use warnings; - -open ( my $has_seq, '>', 'identify_sequences.txt' ) or die $!; -open ( my $no_seq, '>', 'unidentify_sequence.txt' ) or die $!; -my $seq_count = 0; -my $no_seq_count = 0; - -local $/ = 'END:'; - - -while ( <> ) {if ( m/SEQ/ ) { - $seq_count++; - select $has_seq; - } - else { - $no_seq_count++; - select $no_seq; - } -#print current block to selected filehandle. - print; -} -print "SEQ: $seq_count\n"; -print "No SEQ: $no_seq_count\n"; - diff --git a/QC_Export_MGF/QC_MGF_test.Rmd b/QC_Export_MGF/QC_MGF_test.Rmd new file mode 100644 index 0000000..0563798 --- /dev/null +++ b/QC_Export_MGF/QC_MGF_test.Rmd @@ -0,0 +1,477 @@ +--- +title: "Script_QC_MGF" +date: "`r format(Sys.time(), '%d %B, %Y')`" +output: html_document +--- + +```{r, echo=FALSE} +#REPLACE RELEASE 2 WITH THE PATH OF THE NEW RELEASE. + +release1_iden <- file.path(getwd(), "archive_all_2014-10/cache") +#release1_unid <- file.path(getwd(), "archive_all_2014-10/cache") + +release2_iden <- file.path(getwd(), "archive_all_2016-10/archive_identified_2016-10/cache") +release2_unid <- file.path(getwd(),"archive_all_2016-10/archive_unidentified_2016-10/cache") + + +``` + +```{r} +# PRIDE Cluster clusters all MS/MS spectra submitted to PRIDE Archive repository release: 2015-04 +# http://www.ebi.ac.uk/pride/cluster/ + +# Description:The present script provides a reliable QC (Quality control) report about MGF files generated. +# This script must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra + +``` + +```{r, include=FALSE} +# Upload packages +packages <- c( "ggplot2", "scales", "knitr", "markdown", "tidyr", "rmarkdown","gridExtra", "stringr","data.table", "dplyr", "reshape") + +if (length(setdiff(packages, rownames(installed.packages()))) > 0) { + install.packages(setdiff(packages, rownames(installed.packages()))) } + + +library("ggplot2"); library("scales"); library("knitr"); library("markdown"); +library("tidyr"); library("rmarkdown"); library("gridExtra"); library("stringr"); library("data.table"); library("dplyr"); library("reshape") +``` + + +### **Number of peptides: ** +#### **Release 1** + +```{r, echo=FALSE} +#This part reads the files identify and unidentify ID and calculate how many peptides are in the last release +#and the current release +peptides_iden_release1 <- read.table(file.path(release1_iden, "ID_identify.txt"), quote="\"", comment.char="") +peptides_unid_release1 <- read.table(file.path(release1_iden, "ID_unidentify.txt"), quote="\"", comment.char="") + + +peptides_iden_release2 <- read.table(file.path(release2_iden, "ID_identify.txt"), quote="\"", comment.char="") +peptides_unid_release2 <- read.table(file.path(release2_unid, "ID_unidentify.txt"), quote="\"", comment.char="") + + +cat("The number of identified peptides in the release 1 is:", nrow(peptides_iden_release1)) +cat("The number of unidentified peptides in the release 1 is:", nrow(peptides_unid_release1)) + +``` + +```{r, echo=FALSE, results='asis'} +#Print a frequency tables +table_release1 <- data.frame(Types = c("Identified", "Unidentified"), Peptides= c(nrow(peptides_iden_release1),nrow(peptides_unid_release1)) ) + +kable(table_release1, padding = 0) + +``` + +#### **Release 2** + + +```{r, echo=FALSE} +cat("The number of identified peptides in the release 2 is:", nrow(peptides_iden_release2)) +cat("The number of unidentified peptides in the release 2 is:", nrow(peptides_unid_release2)) + + + +``` + +```{r, echo=FALSE, results='asis'} +table_release2 <- data.frame(Types = c("Identified", "Unidentified"), Peptides= c(nrow(peptides_iden_release2),nrow(peptides_unid_release2)) ) + +kable(table_release2, padding = 0) + + + + +``` + +#### **Summary** + +```{r, echo=FALSE, fig.width=10} + +#Conditional +if (nrow(peptides_iden_release1)>nrow(peptides_iden_release2)) { + cat("Number of identified peptides reduced:", nrow(peptides_iden_release1)-nrow(peptides_iden_release2),"\n") +} else if ((nrow(peptides_iden_release1)nrow(peptides_unid_release2)) { + cat("Number of unidentified peptides reduced:", nrow(peptides_iden_release1)-nrow(peptides_iden_release2),"\n") +} else if ((nrow(peptides_unid_release1)nrow(modifications_release2)) { + cat("Number of modifications reduced in the new release:", nrow(modifications_release1)-nrow(modifications_release2),"\n") +} else if ((nrow(modifications_release1)% + full_join(df2, by = "Modifications", suffix = c(".1", ".2")) %>% + # Fix data to convert to character and numeric + mutate_each(funs(as.numeric(as.character(.))), starts_with("pept")) %>% + # See difference + mutate(change = Frequency.2 - Frequency.1) + +#How many new peptides are there in the new release?. +df_peptides <- df_final[is.na(df_final$Frequency.1),] +df_peptides2 <- data.frame(Modifications=df_peptides$Modifications, Frequency=df_peptides$Frequency.2) + +df_peptides3 <- df_final[is.na(df_final$Frequency.2),] +df_peptides4 <- data.frame(Modifications=df_peptides3$Modifications, Frequency=df_peptides3$Frequency.2) + +``` + +```{r, echo=FALSE, warning=FALSE} +#To know if the new release has obtained new peptides. +if (nrow(df_final[is.na(df_final$Frequency.1),])!=0) { + cat("The new release has obtained new peptides") + kable(df_peptides2, padding = 0) +} else if (nrow(df_final[is.na(df_final$Frequency.2),])!=0) { + cat("The new release has lost peptides\n") + kable(df_peptides4, padding = 0) +} else + cat("The new release has got the same peptides") + + + +``` + + +```{r, echo=FALSE} +#HISTOGRAM: +#Para preparar el histograma tenemos que clasificar los tipos de modificaciones, POSICION-DATABA-ID. +# Para ello cogemos los datos que no sean NULL y eliminamos los espacios en banco. + +histo1 = subset(df, Modifications != 'NULL') +histo1[histo1==""] <- NA +histo1 = subset(histo1, Modifications != 'NA') + +histo1_2 = subset(df2, Modifications != 'NULL') +histo1_2[histo1_2==""] <- NA +histo1_2 = subset(histo1_2, Modifications != 'NA') + +#Split dataset. +histo2 <- data.frame(str_split_fixed(histo1$Modifications, ",", 20)) +histo2_2 <- data.frame(str_split_fixed(histo1_2$Modifications, ",", 20)) + +#If you want to check how many columns are empty, you can use the code below: +#columns_emply <- histo2[!sapply(histo2, function(x) all(x == ""))] +#columns_emply <- histo2_2[!sapply(histo2_2, function(x) all(x == ""))] + +#Merge the columns in one. +histo3 <- melt(setDT(histo2), # set df to a data.table + measure.vars = list(c(1:20)), # set column groupings + value.name = 'V')[ # set output name scheme + , -1, with = F] + +histo3_2 <- melt(setDT(histo2_2), # set df to a data.table + measure.vars = list(c(1:20)), # set column groupings + value.name = 'V')[ # set output name scheme + , -1, with = F] + +#Remove white rows. +histo3[histo3==""] <- NA +histo3 = subset(histo3, V1 != " ") + +histo3_2[histo3_2==""] <- NA +histo3_2 = subset(histo3_2, V1 != " ") + +#Remove first part of the string [num]- +histo4 <- data.frame(modifications=gsub(" [A-Za-z] ", "", gsub("[0-9]*-", "", histo3$V1))) +histo4_2 <- data.frame(modifications.2=gsub(" [A-Za-z] ", "", gsub("[0-9]*-", "", histo3_2$V1))) + +#Histograma: +histo5 <- data.frame(table(histo4)) +histo5_2 <- data.frame(table(histo4_2)) + +# ggplot(data=histo5, aes(x=histo4, y=Freq, fill=histo4)) + +# geom_bar(stat="identity") + guides(fill=FALSE)+ +# theme(axis.text.x = element_text(angle = 90, hjust = 1)) +# +# ggplot(data=histo5_2, aes(x=histo4_2, y=Freq, fill=histo4_2)) + +# geom_bar(stat="identity") + guides(fill=FALSE)+ +# theme(axis.text.x = element_text(angle = 90, hjust = 1)) + +``` + +```{r, echo=FALSE, fig.height=15, fig.width=25, message=FALSE, warning=FALSE} +#We're going to compare different releases in order to compare between them and create a stacker plot. + +histo5 <- modifications_release1 +histo5_2 <- modifications_release2 + +colnames(histo5) <- c("Modifications","Frequency") +colnames(histo5_2) <- c("Modifications","Frequency") + +histo6<-merge(histo5,histo5_2, by = "Modifications",all = T) + + +histo7<- melt(histo6) +histo7$variable<-factor(histo7$variable,labels = c("Modifications1","Modifications2")) + + +ggplot(histo7, aes(x = Modifications, y = value, fill = variable)) + + geom_bar(stat = "identity",position = "dodge")+ + theme(axis.text.x = element_text(angle = 20, hjust = 0.5, vjust = -0.1)) + + guides(fill=FALSE)+ + labs("Barplot Release1 vs Release 2") + + xlab("Values")+ + ylab("Frequency")+ + theme(text = element_text(size=18), axis.text.x = element_text(angle = 90, hjust = 1, size = 15), + axis.text.y=element_text(size = 15)) + +``` + +### **Spectrum** + +```{r, echo=FALSE, message=FALSE, warning=FALSE} +#Here is the same than before examples. + +spectrum_iden_release1 <- read.delim(file.path(release1_iden, "tables/spectrum_ide_table.txt"), header = TRUE) +spectrum_unid_release1 <- read.delim(file.path(release1_iden, "tables/spectrum_unide_table.txt"), header=TRUE) + +spectrum_iden_release2 <- read.delim(file.path(release2_iden, "tables/spectrum_ide_table.txt"), header = TRUE) +spectrum_unid_release2 <- read.delim(file.path(release2_unid, "tables/spectrum_unide_table.txt"), header=TRUE) + +``` + +#### **Release 1 ** +```{r, echo=FALSE, message=FALSE, warning=FALSE} +cat("The number of identified spectrum in the release 1 is:", spectrum_iden_release1$Spectrum.Number) +cat("The number of identified spectrum in the release2 is:", spectrum_iden_release2$Spectrum.Number) + +``` + +#### **Release 2** +```{r, echo=FALSE, message=FALSE, warning=FALSE} +cat("The number of identified spectrum in the release 1 is:", spectrum_iden_release1$Spectrum.Number) +cat("The number of identified spectrum in the release2 is:", spectrum_iden_release2$Spectrum.Number) +``` + +#### **Summary** +```{r, echo=FALSE, message=FALSE, warning=FALSE} +#for identified +if (spectrum_iden_release1$Spectrum.Number>spectrum_iden_release2$Spectrum.Number) { + cat("Number of identified spectrum reduced:", spectrum_iden_release1$Spectrum.Number-spectrum_iden_release2$Spectrum.Number,"\n") +} else if ((spectrum_iden_release1$Spectrum.Numberspectrum_unid_release2$Spectrum.Number) { + cat("Number of unidentified spectrum reduced:", spectrum_unid_release1$Spectrum.Number-spectrum_unid_release2$Spectrum.Number,"\n") +} else if ((spectrum_unid_release1$Spectrum.Numbersum(taxonomy_iden_release2$Frequency)) { + cat("Identified peptides from Taxonomy reduced in the new release:", nrow(taxonomy_iden_release1$Frequency)-nrow(taxonomy_iden_release2$Frequency),"\n") +} else if ((sum(taxonomy_iden_release1$Frequency)sum(taxonomy_unid_release2$Frequency)) { + cat("Identified peptides from Taxonomy reduced in the new release:", nrow(taxonomy_unid_release1$Frequency)-nrow(taxonomy_unid_release2$Frequency),"\n") +} else if ((sum(taxonomy_unid_release1$Frequency) + + + + + + + + + + + + +Script_QC_MGF + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
# PRIDE Cluster clusters all MS/MS spectra submitted to PRIDE Archive repository release: 2015-04
+# http://www.ebi.ac.uk/pride/cluster/
+
+# Description:The present script provides a reliable QC (Quality control) report about MGF files generated. 
+# This script must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra
+
+

Number of peptides:

+
+

Release 1

+
## The number of identified peptides in the release 1 is: 1940
+
## The number of unidentified peptides in the release 1 is: 380
+ + + + + + + + + + + + + + + + + +
TypesPeptides
Identified1940
Unidentified380
+
+
+

Release 2

+
## The number of identified peptides in the release 2 is: 102360
+
## The number of unidentified peptides in the release 2 is: 13287
+ + + + + + + + + + + + + + + + + +
TypesPeptides
Identified102360
Unidentified13287
+
+
+

Summary

+
## Number of identified Peptides increased: 100420
+
## Number of unidentified Peptides increased: 12907
+

+
+
+
+

Number of modifications:

+
+

Release 1

+
## There are 3  different modifications
+
## The number of modifications are: 18846
+ + + + + + + + + + + + + + + + + +
ModificationsFrequencyModificationsFrequency
MS:1234121434MOD:003978817
+
+
+

Release 2

+
## There are 3  different modifications
+
## The number of modifications are: 19773
+ + + + + + + + + + + + + + + + + +
ModificationsFrequencyModificationsFrequency
MS:prueba1MOD:0039711177
+
+
+

Summary

+
## The number of identified peptides are equal
+
## The new release has obtained new peptides
+ + + + + + + + + + + + + +
ModificationsFrequency
MS:prueba1
+

+
+
+
+

Spectrum

+
+

Release 1

+
## The number of identified spectrum in the release 1 is: 1940
+
## The number of identified spectrum in the release2  is: 102360
+
+
+

Release 2

+
## The number of identified spectrum in the release 1 is: 1940
+
## The number of identified spectrum in the release2  is: 102360
+
+
+

Summary

+
## Number of identified spectrum Peptides increased: 100420
+
## Number of unidentified spectrum Peptides increased: 12907
+
+
+
+

Taxonomy

+
+

Release 1

+
## Number of species in the release 1 is: 19696
+
## The total taxonomy for identified peptides in the release 1 is: 1940
+
## The total taxonomy for unidentified peptides in the release 1 is:
+
+
+

Release 2

+
## Number of species in the release 1 is: 19696
+
## The total taxonomy for identified peptides in the release 1 is: 102360
+
## The total taxonomy for unidentified peptides in the release 1 is:
+
+
+
+

Summary

+
## Identified peptides from Taxonomy increased in the new release: 0
+
## Unidentified peptides from Taxonomy increased in the new release: 12907
+
+ + + + +
+ + + + + + + + diff --git a/QC_Export_MGF/QC_exporter_run.sh b/QC_Export_MGF/QC_exporter_run.sh new file mode 100644 index 0000000..a58920f --- /dev/null +++ b/QC_Export_MGF/QC_exporter_run.sh @@ -0,0 +1,20 @@ +#!/bin/sh + +##### VARIABLES +# the name to give to the LSF job (to be extended with additional info) +JOB_NAME="QC_MGF_FILES" +# the job parameters that are going to be passed on to the job (build below) +JOB_PARAMETERS="" +# memory limit +MEMORY_LIMIT=40000 +# LSF email notification +JOB_EMAIL="pride-report@ebi.ac.uk" +LOG_FILE_NAME="${JOB_NAME}" +VERSION="2015-04" +QUALITY="2" +OUTPUT_DIRECTORY="/nfs/pride/work/cluster/cluster-file-exporter/" + + +python ./Counter_files.py + +Rscript -e "rmarkdown::render('QC_MGF_test.Rmd')" \ No newline at end of file diff --git a/QC_Export_MGF/Script_QC_MGF.R b/QC_Export_MGF/Script_QC_MGF.R deleted file mode 100644 index 5579c7e..0000000 --- a/QC_Export_MGF/Script_QC_MGF.R +++ /dev/null @@ -1,276 +0,0 @@ -# PRIDE Cluster clusters all MS/MS spectra submitted to PRIDE Archive repository release: 2015-04 -# http://www.ebi.ac.uk/pride/cluster/ - -# Description:The present script provides a reliable QC (Quality control) report about MGF files generated. -# This script must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra - - -# Upload packages -packages <- c( "ggplot2", "scales", "knitr", "markdown", "tidyr", "rmarkdown","gridExtra", "stringr","data.table") -if (length(setdiff(packages, rownames(installed.packages()))) > 0) { - install.packages(setdiff(packages, rownames(installed.packages()))) } - - -library("ggplot2"); library("scales"); library("knitr"); library("markdown"); -library("tidyr"); library("rmarkdown"); library("gridExtra"); library("stringr"); library("data.table") - -### **Files** -#REPLACE RELEASE 2 WITH THE PATH OF THE NEW RELEASE -# release1_iden <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_identified_2016-10" -# release1_unid <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_unidentified_2016-10" -# -# release2_iden <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_identified_2016-10" -# release2_unid <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_unidentified_2016-10" - -release1_iden <- "~/Dropbox/Script_R_Cambridge/Script2/archive_identified_2016-10" -release1_unid <- "~/Dropbox/Script_R_Cambridge/Script2/archive_unidentified_2016-10" - -release2_iden <- "~/Dropbox/Script_R_Cambridge/Script2/archive_identified_2016-10" -release2_unid <- "~/Dropbox/Script_R_Cambridge/Script2/archive_unidentified_2016-10" - - -#Count files how many files are in the folder. -#Load files from last -#file_all <- list.files(file.path(getwd(), "testall"), pattern = "\\.mgf$") -file_iden <- list.files(file.path(getwd(), "archive_identified_2016-10"), pattern = "\\.mgf$") -file_unide <- list.files(file.path(getwd(), "archive_unidentified_2016-10"), pattern = "\\.mgf$") - -#NEW RELEASE. REPLACE WITH THE NEW FOLDER. -file_iden2 <- list.files(file.path(getwd(), "archive_identified_2016-10"), pattern = "\\.mgf$") -file_unide2 <- list.files(file.path(getwd(), "archive_unidentified_2016-10"), pattern = "\\.mgf$") - -#Create a data frame with the data obtained: -df.test <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(file_iden)+length(file_unide)), length(file_iden),length(file_unide))) - -df.test2 <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(file_iden2)+length(file_unide2)), length(file_iden2),length(file_unide2))) - -cat("\nNumber of files in Release 1") -kable(df.test, padding = 0) -cat("\nNumber of files in Release 2") -kable(df.test2, padding = 0) - -df.id_and_uni <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(file_iden),length(file_unide)) ) -df.id_and_uni2 <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(file_iden2),length(file_unide2)) ) - -#Create the pie chart - -a <- ggplot(transform(transform(df.id_and_uni, Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - ggtitle("Release 1") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -b <- ggplot(transform(transform(df.id_and_uni2, Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - ggtitle("Release 2") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -grid.arrange(a, b, ncol=2) - -#Number of files with data. - -setwd(release1_iden) -list_of_iden <- file.info(dir()) -setwd(release1_unid) -list_of_unid <- file.info(dir()) - -setwd(release2_iden) -list_of_iden2 <- file.info(dir()) -setwd(release2_unid) -list_of_unid2 <- file.info(dir()) - - -# Get the size for each file - -setwd(release1_iden) -size_iden <- file.info(dir(path = release1_iden))$size -setwd(release1_unid) -size_uniden <- file.info(dir(path = release1_unid))$size - -setwd(release2_iden) -size_iden2 <- file.info(dir(path = release2_iden))$size -setwd(release1_unid) -size_uniden2 <- file.info(dir(path = release2_unid))$size - - - -# subset the files that have non-zero size -iden_with_data <- rownames(list_of_iden)[which(size_iden != 0)] -unid_with_data <- rownames(list_of_unid)[which(size_uniden != 0)] - -iden_with_data2 <- rownames(list_of_iden2)[which(size_iden2 != 0)] -unid_with_data2 <- rownames(list_of_unid2)[which(size_uniden2 != 0)] - - -# get the empty files -#all_without_data <- rownames(list_of_all)[which(size_all == 0)] -iden_without_data <- rownames(list_of_iden)[which(size_iden == 0)] -unid_without_data <- rownames(list_of_unid)[which(size_uniden == 0)] - -iden_without_data2 <- rownames(list_of_iden2)[which(size_iden2 == 0)] -unid_without_data2 <- rownames(list_of_unid2)[which(size_uniden2 == 0)] - - -### **With data** -#plot with data. - -df_with_data_all <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_with_data)+length(unid_with_data)),length(iden_with_data),length(unid_with_data)) ) -cat("\nNumber of files with identify data") -kable(df_with_data_all, padding = 0) - - -df_with_data_all2 <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_with_data2)+length(unid_with_data2)),length(iden_with_data2),length(unid_with_data2)) ) -cat("\nNumber of files with unidentify data") -kable(df_with_data_all, padding = 0) - - -df_with_data <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_with_data),length(unid_with_data)) ) - -df_with_data2 <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_with_data2),length(unid_with_data2)) ) - -a <- ggplot(transform(transform(df_with_data , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -b <- ggplot(transform(transform(df_with_data2 , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -grid.arrange(a, b, ncol=2) - - -### **Without data** - - -#without data. -df_without_data_all <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_without_data)+length(unid_without_data)),length(iden_without_data),length(unid_without_data)) ) -cat("\nNumber of files without identify data") -kable(df_without_data_all,padding = 0) - -df_without_data_all2 <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_without_data2)+length(unid_without_data2)),length(iden_without_data2),length(unid_without_data2)) ) -cat("\nNumber of files without unidentify data") -kable(df_without_data_all2,padding = 0) - - -df_without_data <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_without_data),length(unid_without_data)) ) - -df_without_data2 <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_without_data2),length(unid_without_data2)) ) - - -a <- ggplot(transform(transform(df_without_data , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -b <- ggplot(transform(transform(df_without_data2 , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -grid.arrange(a, b, ncol=2) - - - -### **Modifications id** - - -setwd("~/Dropbox/Script_R_Cambridge/Script2/cache") -#setwd("/nfs/nobackup/pride/cluster-prod/archive_spectra/cache") -files_to_read <- file.info(dir()) -size <- file.info(dir(path = "~/Dropbox/Script_R_Cambridge/Script2/cache"))$size -#size <- file.info(dir(path = "/nfs/nobackup/pride/cluster-prod/archive_spectra/cache"))$size -files_to_read <- rownames(files_to_read)[which(size != 0)] - -#Use the list a generate -alldfs <- lapply(files_to_read, function(x) { - textfiles <- read.table(x, quote="\"", comment.char="") -}) - -alldfs <- lapply(x = alldfs, seq_along(alldfs), function(x, i) { - assign(paste0(files_to_read[i]), x[[i]], envir=.GlobalEnv) -}) - - - - -#MODIFICATIONS ONLY IN MODIFICATIONS_IDE.TXT -modifications <- data.frame(modifications=gsub("USER03=", "", modifications_ide.txt$V1)) - -modifications_2 <- data.frame(modifications=gsub("USER03=", "", modifications_ide.txt$V1)) - -#Split dataset. -modifications2<- data.frame(str_split_fixed(modifications$modifications, ",", 20)) - - -#If you want to check how many columns are empty, you can use the code below: -#columns_emply <- histo2[!sapply(histo2, function(x) all(x == ""))] -#columns_emply <- histo2_2[!sapply(histo2_2, function(x) all(x == ""))] - -#Merge the columns in one. -modifications3 <- melt(setDT(modifications2), # set df to a data.table - measure.vars = list(c(1:20)), # set column groupings - value.name = 'V')[ # set output name scheme - , -1, with = F] - - -#Remove white rows. -modifications3[modifications3==""] <- NA -modifications3 = subset(modifications3, V1 != " ") - -#Remove first part of the string [num]- -modifications4 <- data.frame(modifications=gsub(" [A-Za-z] ", "", gsub("[0-9]*-", "", modifications3$V1))) - -#Histograma: -modifications5 <- data.frame(table(modifications4)) -kable(modifications5, row.names = FALSE, padding = 0) - - -### **Sequences identified** - - -sequences <- data.frame(sequences=gsub("SEQ=", "", sequences_ide.txt$V1)) -sequences2 <- data.frame(table(sequences)) -cat("\nThere are",nrow(sequences2), "sequences different.\n") -cat("The number of sequences is:", sum(sequences2$Freq)) - - - -### **Spectrum** - - - -spectrum_ide <- data.frame(spectrum_ide=gsub("spectrum=", "", spectrum_ide.txt$V1)) -#Remove strings in the column -spectrum_ide <- data.frame(spectrum_ide=spectrum_ide[grep("[[:digit:]]", spectrum_ide$spectrum_ide), ]) - -spectrum_unid <- data.frame(spectrum_unid=gsub("spectrum=", "", spectrum_unid.txt$V1)) -#Remove strings in the column -spectrum_unid <- data.frame(spectrum_unid=spectrum_unid[grep("[[:digit:]]", spectrum_unid$spectrum_unid), ]) - - -cat("\nThe number of spectrum identified:", sum(as.numeric(spectrum_ide$spectrum_ide))) -cat("\nThe number of spectrum unidentified:", sum(as.numeric(spectrum_unid$spectrum_unid))) - - - -### **Taxonomy** - -taxonomy_ide <- data.frame(spectrum_ide=gsub("TAXONOMY=", "", taxonomy_ide.txt$V1)) - -taxonomy_unide <- data.frame(spectrum_ide=gsub("TAXONOMY=", "", taxonomy_unid.txt$V1)) - - -taxonomy_ide <- data.frame(table(taxonomy_ide)) -taxonomy_unide <- data.frame(table(taxonomy_unide)) - -kable(taxonomy_ide, row.names = FALSE, padding = 0) -kable(taxonomy_unide, row.names = FALSE, padding = 0) - - diff --git a/QC_Export_MGF/Script_QC_MGF.Rmd b/QC_Export_MGF/Script_QC_MGF.Rmd deleted file mode 100644 index e9880fa..0000000 --- a/QC_Export_MGF/Script_QC_MGF.Rmd +++ /dev/null @@ -1,378 +0,0 @@ ---- -title: "**QC metrics MGF**" -date: "`r format(Sys.time(), '%d %B, %Y')`" -output: html_document ---- - -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` - - -```{r} -# PRIDE Cluster clusters all MS/MS spectra submitted to PRIDE Archive repository release: 2015-04 -# http://www.ebi.ac.uk/pride/cluster/ - -# Description:The present script provides a reliable QC (Quality control) report about MGF files generated. -# This script must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra - -``` - -```{r, include=FALSE} -# Upload packages -packages <- c( "ggplot2", "scales", "knitr", "markdown", "tidyr", "rmarkdown","gridExtra", "stringr","data.table") -if (length(setdiff(packages, rownames(installed.packages()))) > 0) { - install.packages(setdiff(packages, rownames(installed.packages()))) } - - -library("ggplot2"); library("scales"); library("knitr"); library("markdown"); -library("tidyr"); library("rmarkdown"); library("gridExtra"); library("stringr"); library("data.table") -``` - -### **Number of files:** -#### **Release 1** - -```{r, echo=FALSE} - -#REPLACE RELEASE 2 WITH THE PATH OF THE NEW RELEASE -release1_iden <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_identified_2016-10" -release1_unid <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_unidentified_2016-10" - -release2_iden <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_identified_2016-10" -release2_unid <- "/nfs/nobackup/pride/cluster-prod/archive_spectra/archive_unidentified_2016-10" - -# release1_iden <- "~/Dropbox/Script_R_Cambridge/Script2/archive_identified_2016-10" -# release1_unid <- "~/Dropbox/Script_R_Cambridge/Script2/archive_unidentified_2016-10" -# -# release2_iden <- "~/Dropbox/Script_R_Cambridge/Script2/archive_identified_2016-10" -# release2_unid <- "~/Dropbox/Script_R_Cambridge/Script2/archive_unidentified_2016-10" -``` - - -```{r, echo=FALSE, results='asis'} - -#Count files how many files are in the folder. -#Load files from last -#file_all <- list.files(file.path(getwd(), "testall"), pattern = "\\.mgf$") -file_iden <- list.files(file.path(getwd(), "archive_identified_2016-10"), pattern = "\\.mgf$") -file_unide <- list.files(file.path(getwd(), "archive_unidentified_2016-10"), pattern = "\\.mgf$") - -#**NEW RELEASE**. REPLACE WITH THE NEW FOLDER. -file_iden2 <- list.files(file.path(getwd(), "archive_identified_2016-10"), pattern = "\\.mgf$") -file_unide2 <- list.files(file.path(getwd(), "archive_unidentified_2016-10"), pattern = "\\.mgf$") - -#Create a data frame with the data obtained: -df.test <- data.frame(Types = c("Total", "Identify", "Unidentify" ), Spectra= c((length(file_iden)+length(file_unide)), length(file_iden),length(file_unide))) - -df.test2 <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(file_iden2)+length(file_unide2)), length(file_iden2),length(file_unide2))) - -kable(df.test, padding = 0) - - -``` - - -#### **Release 2** - -```{r, echo=FALSE, results='asis'} -kable(df.test2, padding = 0) - -``` - -```{r, echo=FALSE, fig.width=10 } -#Create the pie chart - -df.id_and_uni <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(file_iden),length(file_unide)) ) -df.id_and_uni2 <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(file_iden2),length(file_unide2)) ) - - -a <- ggplot(transform(transform(df.id_and_uni, Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - ggtitle("Release 1") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -b <- ggplot(transform(transform(df.id_and_uni2, Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - ggtitle("Release 2") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -grid.arrange(a, b, ncol=2) -``` - -```{r, echo=FALSE} -# create a list of files in the current working directory. CHANGE PATH -#setwd("~/Dropbox/Script_R_Cambridge/Script2/testall") -#list_of_all <- file.info(dir()) -#REPLACE RELEASE 2 WITH THE PATH OF THE NEW RELEASE - - -setwd(release1_iden) -list_of_iden <- file.info(dir()) -setwd(release1_unid) -list_of_unid <- file.info(dir()) - -setwd(release2_iden) -list_of_iden2 <- file.info(dir()) -setwd(release2_unid) -list_of_unid2 <- file.info(dir()) - - -# get the size for each file -#setwd("~/Dropbox/Script_R_Cambridge/Script2/testall") -#size_all <- file.info(dir(path = "~/Dropbox/Script_R_Cambridge/Script2/testall"))$size -setwd(release1_iden) -size_iden <- file.info(dir(path = release1_iden))$size -setwd(release1_unid) -size_uniden <- file.info(dir(path = release1_unid))$size - -setwd(release2_iden) -size_iden2 <- file.info(dir(path = release2_iden))$size -setwd(release1_unid) -size_uniden2 <- file.info(dir(path = release2_unid))$size - - - -# subset the files that have non-zero size -#all_with_data <- rownames(list_of_all)[which(size_all != 0)] -iden_with_data <- rownames(list_of_iden)[which(size_iden != 0)] -unid_with_data <- rownames(list_of_unid)[which(size_uniden != 0)] - -iden_with_data2 <- rownames(list_of_iden2)[which(size_iden2 != 0)] -unid_with_data2 <- rownames(list_of_unid2)[which(size_uniden2 != 0)] - - -# get the empty files -#all_without_data <- rownames(list_of_all)[which(size_all == 0)] -iden_without_data <- rownames(list_of_iden)[which(size_iden == 0)] -unid_without_data <- rownames(list_of_unid)[which(size_uniden == 0)] - -iden_without_data2 <- rownames(list_of_iden2)[which(size_iden2 == 0)] -unid_without_data2 <- rownames(list_of_unid2)[which(size_uniden2 == 0)] - -``` - -### **Files with data** - -#### **Release 1** - -```{r, echo=FALSE, results='asis'} -#plot with data. - -df_with_data_all <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_with_data)+length(unid_with_data)),length(iden_with_data),length(unid_with_data)) ) - -kable(df_with_data_all, padding = 0) -``` -#### **Release 2** - -```{r, echo=FALSE, results='asis' } - -df_with_data_all2 <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_with_data2)+length(unid_with_data2)),length(iden_with_data2),length(unid_with_data2)) ) -kable(df_with_data_all, padding = 0) - -``` - -```{r, echo=FALSE, fig.width=10 } - -df_with_data <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_with_data),length(unid_with_data)) ) - -df_with_data2 <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_with_data2),length(unid_with_data2)) ) - -a <- ggplot(transform(transform(df_with_data , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -b <- ggplot(transform(transform(df_with_data2 , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -grid.arrange(a, b, ncol=2) -``` - -### **Files without data** - -#### **Release 1** - -```{r, echo=FALSE} -#without data. -df_without_data_all <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_without_data)+length(unid_without_data)),length(iden_without_data),length(unid_without_data)) ) -kable(df_without_data_all,padding = 0) - -``` - -#### **Release 2** - -```{r, echo=FALSE } -df_without_data_all2 <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(iden_without_data2)+length(unid_without_data2)),length(iden_without_data2),length(unid_without_data2)) ) -kable(df_without_data_all2,padding = 0) -``` - -```{r, echo=FALSE, fig.width=10 } -df_without_data <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_without_data),length(unid_without_data)) ) - -df_without_data2 <- data.frame(Types = c("Identify", "Unidentify"), Spectra= c(length(iden_without_data2),length(unid_without_data2)) ) - - -a <- ggplot(transform(transform(df_without_data , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -b <- ggplot(transform(transform(df_without_data2 , Spectra=Spectra/sum(Spectra)), labPos=cumsum(Spectra)-Spectra/2), - aes(x="", y = Spectra, fill = Types)) + - geom_bar(width = 1, stat = "identity") + - coord_polar(theta = "y") + - geom_text(aes(y=labPos, label=scales::percent(Spectra)), size=7) - -grid.arrange(a, b, ncol=2) - -``` - -### **Number of modifications: ** -#### **Release 1** - -```{r, echo=FALSE} - -#**Modifications**: - -modifications <- read.delim("/nfs/nobackup/pride/cluster-prod/archive_spectra/cache/modifications_ide_table.txt", header = TRUE) -#modifications <- read.delim("~/Dropbox/Script_R_Cambridge/Script2/tablas/modifications_ide_table.txt", header = TRUE) - -colnames(modifications) <- c("Modifications", "Frequency") -modifications <- modifications[order(modifications$Modifications),] - -modifications <- cbind(modifications[1:(nrow(modifications)/2),], modifications[((nrow(modifications)/2)+1):nrow(modifications),]) -#modifications2 <- cbind(modifications2[1:(nrow(modifications2)/2),],modifications2[((nrow(modifications2)/2)+1):nrow(modifications2),]) - -cat("There are",nrow(modifications), "modifications different.") -cat("The number of modifications is:", sum(modifications$Frequency)) -kable(modifications, row.names = FALSE, padding = 0) -``` - -#### **Release 2** - -```{r, echo=FALSE} - -cat("There are",nrow(modifications), "modifications different.") -cat("The number of modifications is:", sum(modifications$Frequency)) - -Kable(modifications, row.names = FALSE, padding = 0) - - -``` - -### **Sequences identified** - -```{r, include=FALSE} - -#Sequences -sequences<-fread(path.expand("/nfs/nobackup/pride/cluster-prod/archive_spectra/cache/sequences_ide_table.txt"), sep="auto", header = FALSE) -#sequences<-fread(path.expand("~/Dropbox/Script_R_Cambridge/Script2/tablas/sequences_ide_table.txt"), sep="auto", header = FALSE) -colnames(sequences) <- c("Sequences", "Frequency") - -``` - -#### **Release 1** - -```{r, echo=FALSE} -cat("There are",nrow(sequences), "sequences different.") -cat("The number of sequences is:", sum(sequences$Frequency)) -``` - -#### **Release 2** - -```{r, echo=FALSE} -cat("There are",nrow(sequences), "sequences different.") -cat("The number of sequences is:", sum(sequences$Frequency)) -``` - -### **Spectrum** -#### **Release 1** - -```{r, echo=FALSE} - -#Spectrum -Spectrum <- read.delim("/nfs/nobackup/pride/cluster-prod/archive_spectra/cache/spectrum_table.txt", header = FALSE) -#Spectrum <- read.delim("~/Dropbox/Script_R_Cambridge/Script2/tablas/spectrum_table.txt", header = FALSE) - - - cat("The number of spectrum identified is:", Spectrum$V1) - cat("The number of spectrum unidentified is:", Spectrum$V2) - -``` - -#### **Release 2** - -```{r, echo=FALSE} - -#Spectrum -Spectrum <- read.delim("/nfs/nobackup/pride/cluster-prod/archive_spectra/cache/spectrum_table.txt", header = FALSE) -#Spectrum <- read.delim("~/Dropbox/Script_R_Cambridge/Script2/tablas/spectrum_table.txt", header = FALSE) - - - cat("The number of spectrum identified is:", Spectrum$V1) - cat("The number of spectrum unidentified is:", Spectrum$V2) - -``` - -### **Taxonomy** -#### **Release 1** - -```{r, echo=FALSE, results='asis'} - -#Taxonomy -taxonomy_ide <- read.delim("/nfs/nobackup/pride/cluster-prod/archive_spectra/cache/taxonomy_ide_table.txt", header = FALSE) -#taxonomy_ide <- read.delim("~/Dropbox/Script_R_Cambridge/Script2/tablas/taxonomy_ide_table.txt", header = FALSE) - -colnames(taxonomy_ide) <- c("Taxonomy", "Frequency") - -taxonomy_ide <- taxonomy_ide[order(-taxonomy_ide$Frequency),] - -taxonomy_ide <- cbind(taxonomy_ide[1:(nrow(taxonomy_ide)/2),], taxonomy_ide[((nrow(taxonomy_ide)/2)+1):nrow(taxonomy_ide),]) - -kable(taxonomy_ide, row.names = FALSE, padding = 0) - -``` - -#### **Release 2** - -```{r, echo=FALSE, results='asis'} -taxonomy_unide <- read.delim("/nfs/nobackup/pride/cluster-prod/archive_spectra/cache/taxonomy_unide_table.txt", header = FALSE) -#taxonomy_unide <- read.delim("~/Dropbox/Script_R_Cambridge/Script2/tablas/taxonomy_unide_table.txt", header = FALSE) -colnames(taxonomy_unide) <- c("Taxonomy", "Frequency") -taxonomy_unide <- taxonomy_unide[order(-taxonomy_unide$Frequency),] -taxonomy_unide <- cbind(taxonomy_unide[1:(nrow(taxonomy_unide)/2),], taxonomy_ide[((nrow(taxonomy_unide)/2)+1):nrow(taxonomy_unide),]) -kable(taxonomy_unide, row.names = FALSE, padding = 0) - -``` - -### **Number of peptides** - -```{r} - -nrow(modifications_ide_table) - -#Create a data frame with the data obtained: -df.test <- data.frame(Types = c("Total", "Identify", "Unidentify" ), Spectra= c((length(file_iden)+length(file_unide)), length(file_iden),length(file_unide))) - -df.test2 <- data.frame(Types = c("Total", "Identify", "Unidentify"), Spectra= c((length(file_iden2)+length(file_unide2)), length(file_iden2),length(file_unide2))) - -kable(df.test, padding = 0) - - - - -``` - - - - - - - diff --git a/QC_Export_MGF/Script_QC_MGF.html b/QC_Export_MGF/Script_QC_MGF.html deleted file mode 100644 index 2379249..0000000 --- a/QC_Export_MGF/Script_QC_MGF.html +++ /dev/null @@ -1,12302 +0,0 @@ - - - - - - - - - - - - - -QC metrics MGF - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# PRIDE Cluster clusters all MS/MS spectra submitted to PRIDE Archive repository release: 2015-04
-# http://www.ebi.ac.uk/pride/cluster/
-
-# Description:The present script provides a reliable QC (Quality control) report about MGF files generated. 
-# This script must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra
-
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Number of files:

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Release 1

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TypesSpectra
Total2432
Identify1212
Unidentify1220
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TypesSpectra
Total2432
Identify1212
Unidentify1220
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Files with data

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Release 1

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TypesSpectra
Total1884
Identify1019
Unidentify865
#### **Release 2**
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TypesSpectra
Total1884
Identify1019
Unidentify865
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Files without data

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Release 1

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TypesSpectra
Total548
Identify193
Unidentify355
#### **Release 2**
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TypesSpectra
Total548
Identify193
Unidentify355
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Number of modifications:

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Release 1

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## There are 822 modifications different.
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## The number of modifications is: 52915702
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Release 2

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## There are 822 modifications different.
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## The number of modifications is: 52915702
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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ModificationsFrequencyModificationsFrequency
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-
-
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-

Sequences identified

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-

Release 1

-
## There are 19924297 sequences different.
-
## The number of sequences is: 296442947
-
-
-

Release 2

-
## There are 19924297 sequences different.
-
## The number of sequences is: 296442947
-
-
-
-

Spectrum

-
-

Release 1

-
## The number of spectrum identified is: 133466478
-
## The number of spectrum unidentified is: 302832941
-
-
-

Release 2

-
## The number of spectrum identified is: 133466478
-
## The number of spectrum unidentified is: 302832941
-
-
-
-

Taxonomy

-
-

Release 1

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
TaxonomyFrequencyTaxonomyFrequency
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135062310672945919
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570229744176013
1454812903823510
10806128717894623
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-

Release 2

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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-
-
- - - - -
- - - - - - - - diff --git a/QC_Export_MGF/counter.py b/QC_Export_MGF/counter.py deleted file mode 100644 index d53764e..0000000 --- a/QC_Export_MGF/counter.py +++ /dev/null @@ -1,39 +0,0 @@ -# -*- coding: utf-8 -*- - -#Script to create frequency tables. - -#Modifications -from collections import Counter -with open('modifications_ide_final.txt') as f1,open('modifications_ide_table.txt','w') as f2: - c=Counter(x.strip() for x in f1) - for x in c: - f2.write("%s\t%s\n" % ( x,str(c[x])) ) # - -#Sequences -from collections import Counter -with open('sequences_ide_final.txt') as f1,open('sequences_ide_table.txt','w') as f2: - c=Counter(x.strip() for x in f1) - for x in c: - f2.write("%s\t%s\n" % ( x,str(c[x])) ) - -#Spectrum count: -from collections import Counter -with open('spectrum_ide.txt') as f1,open('spectrum_unide.txt') as f2, open('spectrum_table.txt','w') as f3: - lines1 = f1.read().count('\n') - lines2 = f2.read().count('\n') - f3.write("%s\t%s\n" % ( lines1, lines2 )) - - -#Taxonomy ide: -from collections import Counter -with open('taxonomy_ide.txt') as f1,open('taxonomy_ide_table.txt','w') as f2: - c=Counter(x.strip() for x in f1) - for x in c: - f2.write("%s\t%s\n" % ( x,str(c[x])) ) - -#Taxonomy unide: -from collections import Counter -with open('taxonomy_unide.txt') as f1,open('taxonomy_unide_table.txt','w') as f2: - c=Counter(x.strip() for x in f1) - for x in c: - f2.write("%s\t%s\n" % ( x,str(c[x])) ) \ No newline at end of file diff --git a/README.md b/README.md index 3d27992..fa01a06 100644 --- a/README.md +++ b/README.md @@ -2,26 +2,43 @@ ## QC for MGF files -The script for the QC of the MGF files ( Files obtained after the import of Data from PRIDE Archive) is in this repo in github(). -This script Script_QC_MGF.Rmd must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra to be run. The path of the folder with the data generated from the current release should be changed inside the script. +The script for the QC of the MGF files ( Files obtained after the import of Data from PRIDE Archive) is in this repo in github(https://github.com/PRIDE-Cluster/pride-cluster-qc/tree/master/QC_Export_MGF). +This QC is made by different script that must be runned orderly. Firstly: Counter_files.py and .Rmd. In order to facilitate this, a script has been created in bash that automatically executes these scripts. +These scripts must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra to be run. The path of the folder with the data generated from the current release should be changed inside the scripts. The output file will be a html file with the following informations - - Number of files (Total, identified, unidentified) in both releases. - - Percent graph - - Number of modifications + - Number of peptides in both releases (Identified, unidentified). + - Graphs that show the differences between both releases + - Number of modifications and new ones. - Total number of modifications and frequency. - - Sequences identified in both releases. + - Number of identified and unidentified spectrum + - Number of species in both releases - Number of spectrum identified and unidentified - Taxonomy. + - Stacked barplot of the taxonomy. -To generate the QC report, run the script ./Script_QC_MGF.sh +To generate the QC report, run the script ./QC_exporter_run.sh ## QC Clustering files +The python application to do a QC of the clustering files is: ./spectra-cluster-py-comparer-dev/spectra_cluster/ui/cluster_comparer_cli.py +To run this application you have to change the path of the total_clustering.file in "input" and choose a path for the output. + +./spectra-cluster-py-comparer-dev/spectra_cluster/ui/cluster_comparer_cli.py --input ./archive_clustering_all-2014-10/final.clustering,./archive_clustering_all-2014-10/final.clustering --output comparer.txt + +#### IMPORTANT +The final_clustering file must be created by merging all files. This is done easily from the terminal and typing: + cat *.clustering > ./total.clustering + +Sometimes, some spectra are repeated, which should not happen. If this happens, the duplicates must be deleted. For them there are two different applications written in perl and in python. My recommendation is to use Perl, since the execution time is shorter. +To run the perl script just type: + perl duplicate_remover.pl final.clustering.file + + ## QC for Spectrum libraries ## QC for Peptides Report -The script for the Peptides Report (.tsv files) is in this repo in github(). +The script for the Peptides Report (.tsv files) is in this repo in github(https://github.com/PRIDE-Cluster/pride-cluster-qc/tree/master/QC_Peptide_Reports). Information about: This pipeline generate a html file with the following information: @@ -35,4 +52,5 @@ Information about: This pipeline generate a html file with the following informa To run the script QC_metrics_report.Rmd, this should be in the folder /nfs/pride/work/cluster. - To create the QC report you should change the path of the file that you are interesting to analyze. - - Run the script ./QC_metrics_report.sh + - Run the script ./reporterScript.sh + From d331cb6eaff4aa71a0fa8eb6af9e679a2e473f2b Mon Sep 17 00:00:00 2001 From: Enrique Date: Fri, 31 Mar 2017 11:13:58 +0100 Subject: [PATCH 3/3] Improved documentations --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index fa01a06..945488f 100644 --- a/README.md +++ b/README.md @@ -2,8 +2,8 @@ ## QC for MGF files -The script for the QC of the MGF files ( Files obtained after the import of Data from PRIDE Archive) is in this repo in github(https://github.com/PRIDE-Cluster/pride-cluster-qc/tree/master/QC_Export_MGF). -This QC is made by different script that must be runned orderly. Firstly: Counter_files.py and .Rmd. In order to facilitate this, a script has been created in bash that automatically executes these scripts. +The script for the QC of the MGF files ( Files obtained after the import of Data from PRIDE Archive) is in this repository in github(https://github.com/PRIDE-Cluster/pride-cluster-qc/tree/master/QC_Export_MGF). +This QC is consists of different scripts that must be run orderly. Firstly: Counter_files.py and, Secondly .Rmd. In order to facilitate this, a script has been created in bash that automatically executes these scripts. These scripts must be in the folder /nfs/nobackup/pride/cluster-prod/archive_spectra to be run. The path of the folder with the data generated from the current release should be changed inside the scripts. The output file will be a html file with the following informations - Number of peptides in both releases (Identified, unidentified). @@ -38,9 +38,9 @@ To run the perl script just type: ## QC for Peptides Report -The script for the Peptides Report (.tsv files) is in this repo in github(https://github.com/PRIDE-Cluster/pride-cluster-qc/tree/master/QC_Peptide_Reports). +The script for the Peptides Report (.tsv files) is in this repository in github(https://github.com/PRIDE-Cluster/pride-cluster-qc/tree/master/QC_Peptide_Reports). -Information about: This pipeline generate a html file with the following information: +Information about: This pipeline generate an html file with the following information: - Repeated Sequences Results: This should be always 0. - Number of peptides and their increase or decrease.