changeset 15:d1d20f341632 draft

fastqc_report v2.0.0

--- a/fastqc_report.Rmd	Wed Oct 18 22:06:39 2017 -0400
+++ b/fastqc_report.Rmd	Thu Oct 19 00:11:14 2017 -0400
@@ -1,5 +1,5 @@
 ---
-title: 'HTML report title'
+title: 'Short reads evaluation with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)'
 output:
     html_document:
       number_sections: true
@@ -35,18 +35,47 @@
 done
 ```
 
-* Create links to original HTML reports
+## Evaluation results
 
 ```{r 'html report links'}
-html_report_list = list()
-html_files = list.files('REPORT_DIR', pattern = '.*html')
-for (i in html_files) {
-  html_report_list[[i]] = tags$li(tags$a(href=i, i))
-}
-tags$ul(html_report_list)
+html_file = list.files('REPORT_DIR', pattern = '.*html')
+tags$ul(tags$a(href=html_file, paste0('HTML report', opt$name)))
+```
+
+
+```{r 'extract fastqc_data.txt and summary.txt'}
+# list all zip files
+zip_file = list.files(path = 'REPORT_DIR', pattern = '.zip')
+unzip(paste0('REPORT_DIR/', zip_file), exdir = 'REPORT_DIR')
+
+unzip_directory = paste0(tail(strsplit(opt$reads, '/')[[1]], 1), '_fastqc/')
+fastqc_data_txt_path = paste0('REPORT_DIR/', unzip_directory, 'fastqc_data.txt')
+summary_txt_path = paste0('REPORT_DIR/', unzip_directory, 'summary.txt')
 ```
 
-# Fastqc output summary
+
+```{r 'summary.txt'}
+tags$ul(tags$a(href=paste0(unzip_directory, 'summary.txt'), 'summary.txt'))
+```
+
+
+```{r 'fastqc_data.txt'}
+tags$ul(tags$a(href=paste0(unzip_directory, 'fastqc_data.txt'), 'fastqc_data.txt'))
+```
+
+
+# Fastqc output visualization
+
+## Overview
+
+```{r}
+# read.table(fastqc_data_txt_path)
+summary_txt = read.csv(summary_txt_path, header = FALSE, sep = '\t')[, 2:1]
+names(summary_txt) = c('MODULE', 'PASS/FAIL')
+knitr::kable(summary_txt)
+```
+
+## Summary by module {.tabset}
 
 * Define a function to extract outputs for each module from fastqc output
 
@@ -62,7 +91,21 @@
 }
 ```
 
-## 
+### Per base sequence quality
+
+```{r}
+pbsq = extract_data_module(fastqc_data_txt_path, 'Per base sequence quality')
+knitr::kable(pbsq)
+```
+
+### Per tile sequence quality
+
+```{r}
+ptsq = extract_data_module(fastqc_data_txt_path, 'Per tile sequence quality')
+knitr::kable(ptsq)
+```
+
+
 
 # Session Info
 

--- a/fastqc_report.xml	Wed Oct 18 22:06:39 2017 -0400
+++ b/fastqc_report.xml	Thu Oct 19 00:11:14 2017 -0400
@@ -30,6 +30,7 @@
         Rscript '${__tool_directory__}/fastqc_report_render.R'
             -e $echo
             -r $reads
+            -n $reads.name
 
 		    -o $report
 		    -d $report.files_path

--- a/fastqc_report_ori.Rmd	Wed Oct 18 22:06:39 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,381 +0,0 @@
----
-title: "Fastqc report: short reads quality evaluation"
-author: "Ming Chen"
-output: html_document
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo=ECHO, warning=FALSE, message=FALSE)
-library(plyr)
-library(stringr)
-library(dplyr)
-library(highcharter)
-library(DT)
-library(reshape2)
-library(plotly)
-library(formattable)
-library(htmltools)
-```
-
-
-```{bash 'create output directory', echo=FALSE}
-# create extra files directory. very important!
-mkdir REPORT_OUTPUT_DIR
-```
-
-# Fastqc analysis
-```{bash 'copy data to working directory', echo=FALSE}
-# Copy uploaded data to the working directory
-for f in $(echo READS | sed "s/,/ /g")
-do
-    cp $f ./
-done
-```
-
-
-```{bash 'run fastqc', echo=FALSE}
-for r in $(ls *.dat)
-do
-    fastqc -o REPORT_OUTPUT_DIR $r > /dev/null 2>&1
-done
-```
-
-## Fastqc html reports
-
-Below are links to ***Fastqc*** original html reports.
-```{r 'html report links'}
-html_report_list = list()
-html_files = list.files('REPORT_OUTPUT_DIR', pattern = '.*html')
-for (i in html_files) {
-  html_report_list[[i]] = tags$li(tags$a(href=i, i))
-}
-tags$ul(html_report_list)
-```
-
-
-## Parsing fastqc data
-
-```{bash echo=FALSE}
-##==== copy fastqc generated zip files from report output directory to job work directory ==
-cp -r REPORT_OUTPUT_DIR/*zip ./
-
-# create a file to store data file paths
-echo "sample_id,file_path" > PWF_file_paths.txt # Pass, Warning, Fail
-echo "sample_id,file_path" > PBQS_file_paths.txt # Per Base Quality Score
-echo "sample_id,file_path" > PSQS_file_paths.txt # Per Sequence Quality Score
-echo "sample_id,file_path" > PSGC_file_paths.txt # Per Sequence GC Content
-echo "sample_id,file_path" > PBSC_file_paths.txt # Per Base Sequence Content
-echo "sample_id,file_path" > PBNC_file_paths.txt # Per Base N Content
-echo "sample_id,file_path" > SDL_file_paths.txt # Sequence Duplication Level
-echo "sample_id,file_path" > SLD_file_paths.txt # Sequence Length Distribution
-echo "sample_id,file_path" > KMC_file_paths.txt # Kmer Content
-
-for i in $(ls *.zip)
-do
-    BASE=$(echo $i | sed 's/\(.*\)\.zip/\1/g')
-    echo $BASE
-    unzip ${BASE}.zip > /dev/null 2>&1
-    
-    ##====== pass,warning,fail (WSF) =============
-    awk '/^>>/ {print}' "$BASE"/fastqc_data.txt | grep -v 'END_MODULE' | sed 's/>>//' > "$BASE"-PWF.txt
-    echo "${BASE},${BASE}-PWF.txt" >> PWF_file_paths.txt
-
-    ##====== per base quality scores (PBQS) ======
-    awk '/^>>Per base sequence quality/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBQS.txt
-    echo "${BASE},${BASE}-PBQS.txt" >> PBQS_file_paths.txt
-
-    ##====== per sequence quality scores (PSQS)
-    awk '/^>>Per sequence quality scores/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSQS.txt
-    echo "${BASE},${BASE}-PSQS.txt" >> PSQS_file_paths.txt
-
-    ##====== Per sequence GC content (PSGC)
-    awk '/^>>Per sequence GC content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSGC.txt
-    echo "${BASE},${BASE}-PSGC.txt" >> PSGC_file_paths.txt
-    
-    ##====== Per Base Sequence Content (PBSC)
-    awk '/^>>Per base sequence content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBSC.txt
-    echo "${BASE},${BASE}-PBSC.txt" >> PBSC_file_paths.txt
-    
-    ##====== Per Base N Content (PBNC)
-    awk '/^>>Per base N content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBNC.txt
-    echo "${BASE},${BASE}-PBNC.txt" >> PBNC_file_paths.txt
-    
-    ##====== Sequence Duplication Level (SDL)
-    awk '/^>>Sequence Duplication Levels/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SDL.txt
-    echo "${BASE},${BASE}-SDL.txt" >> SDL_file_paths.txt
-    
-    ##====== Sequence Length Distribution (SLD)
-    awk '/^>>Sequence Length Distribution/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SLD.txt
-    echo "${BASE},${BASE}-SLD.txt" >> SLD_file_paths.txt
-    
-    ##====== Kmer Content ============
-    awk '/^>>Kmer Content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-KMC.txt
-    echo "${BASE},${BASE}-KMC.txt" >> KMC_file_paths.txt
-    
-done
-```
-
-
-## Evaluation Overview
-
-```{r 'overview'}
-PWF_file_paths = read.csv('PWF_file_paths.txt',
-                           header = TRUE, stringsAsFactors = FALSE)
-rm('PWF_df')
-for(i in 1:nrow(PWF_file_paths)) {
-  file_path = PWF_file_paths[i,2]
-  pwf_df = read.csv(file_path,
-                     sep='\t', header=FALSE, stringsAsFactors = FALSE)
-  colnames(pwf_df) = c('item', PWF_file_paths[i,1])
-  if (!exists('PWF_df')) {
-    PWF_df = pwf_df
-  } else {
-    PWF_df = cbind(PWF_df, pwf_df[,2,drop=FALSE])
-  }
-}
-```
-
-```{r}
-my_icon = c('ok', 'remove', 'star')
-names(my_icon) = c('pass', 'fail', 'warn')
-evaluate_list = list()
-for (i in colnames(PWF_df)[-1]) {
-  evaluate_list[[i]] = formatter(
-      "span", 
-      style = x ~ style("background-color" = ifelse(x =='pass', '#9CD027', ifelse(x == 'fail', '#CC0000', '#FF4E00')), 
-                        "color" = "white",
-                        "width" = "50px",
-                        "float" = "left",
-                        "padding-right" = "5px")
-    )
-}
-
-formattable(PWF_df, evaluate_list)
-```
-
-
-## Per Base Quality Scores
-
-```{r}
-PBQS_df = data.frame()
-PBQS_file_paths = read.csv('PBQS_file_paths.txt',
-                           header = TRUE, stringsAsFactors = FALSE)
-for(i in 1:nrow(PBQS_file_paths)) {
-  # file_path = paste0('REPORT_OUTPUT_DIR/', PBQS_file_paths[i,2])
-  file_path = PBQS_file_paths[i,2]
-  pbqs_df = read.csv(file_path,
-                     sep='\t', header=TRUE, stringsAsFactors = FALSE) %>%
-    mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]),
-           Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>%
-  (function (df) {
-    df1 = select(df, -Base2)
-    df2 = select(df, -Base1) %>% filter(Base2 != '')
-    colnames(df1) = c(colnames(df1)[1:7], 'Base')
-    colnames(df2) = c(colnames(df2)[1:7], 'Base')
-    res = rbind(df1, df2) %>% arrange(Base)
-    return(res)
-  })
-  pbqs_df$sample_id = rep(PBQS_file_paths[i,1], nrow(pbqs_df))
-  PBQS_df = rbind(PBQS_df, pbqs_df)
-}
-```
-
-
-```{r}
-# datatable(PBQS_df)
-max_phred = max(PBQS_df$Mean) + 10
-hchart(PBQS_df, "line", hcaes(x = Base, y = Mean, group = sample_id)) %>%
-  hc_title(
-    text = "Per Base Quality Score"
-  ) %>%
-  hc_yAxis(
-    title = list(text = "Mean Base Quality Score"),
-    min = 0,
-    max = max_phred,
-    plotLines = list(
-      list(label = list(text = "Phred Score = 27"),
-           width = 2,
-           dashStyle = "dash",
-           color = "green",
-           value = 27),
-      list(label = list(text = "Phred Score = 20"),
-           width = 2,
-           color = "red",
-           value = 20)
-    )
-  ) %>% 
-  hc_exporting(enabled = TRUE)
-```
-
-
-## Per Base N Content
-
-```{r}
-PBNC_df = data.frame()
-PBNC_file_paths = read.csv('PBNC_file_paths.txt',
-                           header = TRUE, stringsAsFactors = FALSE)
-for(i in 1:nrow(PBNC_file_paths)) {
-  # file_path = paste0('REPORT_OUTPUT_DIR/', PBNC_file_paths[i,2])
-  file_path = PBNC_file_paths[i,2]
-  pbnc_df = read.csv(file_path,
-                     sep='\t', header=TRUE, stringsAsFactors = FALSE) %>%
-    mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]),
-           Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>%
-  (function (df) {
-    df1 = select(df, -Base2)
-    df2 = select(df, -Base1) %>% filter(Base2 != '')
-    colnames(df1) = c(colnames(df1)[1:2], 'Base')
-    colnames(df2) = c(colnames(df2)[1:2], 'Base')
-    res = rbind(df1, df2) %>% arrange(Base)
-    return(res)
-  })
-  pbnc_df$sample_id = rep(PBNC_file_paths[i,1], nrow(pbnc_df))
-  PBNC_df = rbind(PBNC_df, pbnc_df)
-}
-```
-
-
-```{r}
-PBNC_df$N.Count = PBNC_df$N.Count * 100
-max_phred = max(PBNC_df$N.Count) + 5
-hchart(PBNC_df, "line", hcaes(x = as.character(Base), y = N.Count, group = sample_id)) %>%
-  hc_title(
-    text = "Per Base N Content"
-  ) %>%
-  hc_xAxis(
-    title = list(text = "Base Position")
-  ) %>%
-  hc_yAxis(
-    title = list(text = "N %"),
-    plotLines = list(
-      list(label = list(text = "N = 5%"),
-           width = 2,
-           dashStyle = "dash",
-           color = "red",
-           value = 5)
-    )
-  ) %>% 
-  hc_exporting(enabled = TRUE)
-```
-
-
-
-
-## Per Sequence Quality Scores
-
-```{r}
-PSQS_df = data.frame()
-PSQS_file_paths = read.csv('PSQS_file_paths.txt', 
-                           header = TRUE, stringsAsFactors = FALSE)
-for(i in 1:nrow(PSQS_file_paths)) {
-  # file_path = paste0('REPORT_OUTPUT_DIR/', PSQS_file_paths[i,2])
-  file_path = PSQS_file_paths[i,2]
-  psqs_df = read.csv(file_path,
-                     sep='\t', header=TRUE, stringsAsFactors = FALSE) 
-  psqs_df$sample_id = rep(PSQS_file_paths[i,1], nrow(psqs_df))
-  PSQS_df = rbind(PSQS_df, psqs_df)
-}
-```
-
-
-```{r}
-max_phred = max(PSQS_df$X.Quality) + 5
-hchart(PSQS_df, "line", hcaes(x = X.Quality, y = Count, group = sample_id)) %>%
-  hc_title(
-    text = "Per Sequence Quality Score"
-  ) %>%
-  hc_xAxis(
-    title = list(text = "Mean Sequence Quality Score"),
-    min = 0,
-    max = max_phred,
-    plotLines = list(
-      list(label = list(text = "Phred Score = 27"),
-           width = 2,
-           dashStyle = "dash",
-           color = "green",
-           value = 27),
-      list(label = list(text = "Phred Score = 20"),
-           width = 2,
-           color = "red",
-           value = 20)
-    )
-  ) %>% 
-  hc_exporting(enabled = TRUE)
-```
-
-
-## Per Sequence GC Content
-
-
-```{r}
-PSGC_df = data.frame()
-PSGC_file_paths = read.csv('PSGC_file_paths.txt', 
-                           header = TRUE, stringsAsFactors = FALSE)
-for(i in 1:nrow(PSGC_file_paths)) {
-  # file_path = paste0('REPORT_OUTPUT_DIR/', PSGC_file_paths[i,2])
-  file_path = PSGC_file_paths[i,2]
-  psgc_df = read.csv(file_path,
-                     sep='\t', header=TRUE, stringsAsFactors = FALSE) 
-  psgc_df$sample_id = rep(PSGC_file_paths[i,1], nrow(psgc_df))
-  PSGC_df = rbind(PSGC_df, psgc_df)
-}
-```
-
-
-```{r}
-max_phred = max(PSGC_df$Count) + 5
-hchart(PSGC_df, "line", hcaes(x = X.GC.Content, y = Count, group = sample_id)) %>%
-  hc_title(
-    text = "Per Sequence GC Content"
-  ) %>%
-  hc_xAxis(
-    title = list(text = "% GC")
-  ) %>%
-  hc_exporting(enabled = TRUE)
-```
-
-
-## Per Base Sequence Content
-
-```{r}
-PBSC_df = data.frame()
-PBSC_file_paths = read.csv('PBSC_file_paths.txt',
-                           header = TRUE, stringsAsFactors = FALSE)
-for(i in 1:nrow(PBSC_file_paths)) {
-  # file_path = paste0('REPORT_OUTPUT_DIR/', PBSC_file_paths[i,2])
-  file_path = PBSC_file_paths[i,2]
-  pbsc_df = read.csv(file_path,
-                     sep='\t', header=TRUE, stringsAsFactors = FALSE) %>%
-    mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]),
-           Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>%
-  (function (df) {
-    df1 = select(df, -Base2)
-    df2 = select(df, -Base1) %>% filter(Base2 != '')
-    colnames(df1) = c(colnames(df1)[1:5], 'Base')
-    colnames(df2) = c(colnames(df2)[1:5], 'Base')
-    res = rbind(df1, df2) %>% arrange(Base)
-    return(res)
-  })
-  pbsc_df$sample_id = rep(PBSC_file_paths[i,1], nrow(pbsc_df))
-  PBSC_df = rbind(PBSC_df, pbsc_df)
-}
-```
-
-
-```{r out.width="100%"}
-PBSC_df_2 = select(PBSC_df, -X.Base) %>%
-  melt(id = c('Base', 'sample_id'), value.name = 'base_percentage')
-p = ggplot(data = PBSC_df_2, aes(x = Base, y = base_percentage, group = variable, color = variable)) +
-  geom_line() +
-  facet_wrap(~ sample_id)
-ggplotly(p)
-```
-
-
-# Session Info
-
-```{r 'session info'}
-sessionInfo()
-```
-
-

--- a/fastqc_report_render.R	Wed Oct 18 22:06:39 2017 -0400
+++ b/fastqc_report_render.R	Thu Oct 19 00:11:14 2017 -0400
@@ -40,12 +40,13 @@
   ##------- 1. input data ---------------------
   args_list$ECHO = c('echo', 'e', '1', 'character')
   args_list$READS = c('reads', 'r', '1', 'character')
+  args_list$NAMES = c('names', 'n', '1', 'character')
   ##--------2. output report and outputs --------------
-  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
+  args_list$REPORT_HTML = c('report_html', 'o', '1', 'character')
   args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
   args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
   ##--------3. .Rmd templates in the tool directory ----------
-  args_list$FASTQC_REPORT_RMD = c('fastqc_report_rmd', 't', '1', 'character')
+  args_list$FASTQC_REPORT_RMD = c('fastqc_report_rmd', 'p', '1', 'character')
   ##-----------------------------------------------------------
   opt = getopt(t(as.data.frame(args_list)))
 
@@ -68,7 +69,7 @@
       gsub('READS', opt$reads, x)
     }) %>%
     (function(x) {
-      gsub('REPORT_DIR', opt$output_dir, x)
+      gsub('REPORT_DIR', opt$report_dir, x)
     }) %>%
     (function(x) {
       fileConn = file('fastqc_report.Rmd')

--- a/fastqc_report_render_ori.R	Wed Oct 18 22:06:39 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-##======= Handle arguments from command line ========
-# setup R error handline to go to stderr
-options(show.error.messages = FALSE,
-error = function(){
-    cat(geterrmessage(), file = stderr())
-    quit("no", 1, F)
-})
-
-# we need that to not crash galaxy with an UTF8 error on German LC settings.
-loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-# suppress warning
-options(warn = - 1)
-
-options(stringsAsFactors = FALSE, useFancyQuotes = FALSE)
-args = commandArgs(trailingOnly = TRUE)
-
-suppressPackageStartupMessages({
-    library(getopt)
-    library(tools)
-})
-
-# column 1: the long flag name
-# column 2: the short flag alias. A SINGLE character string
-# column 3: argument mask
-#           0: no argument
-#           1: argument required
-#           2: argument is optional
-# column 4: date type to which the flag's argument shall be cast.
-#           possible values: logical, integer, double, complex, character.
-spec_list = list()
-spec_list$READS = c('reads', 'r', '1', 'character')
-spec_list$ECHO = c('echo', 'e', '1', 'character')
-spec_list$FASTQC_TPL = c('fastqc_tpl', 'p', 1, 'character')
-spec_list$REPORT = c('report', 'o', '1', 'character')
-spec_list$REPORT_OUTPUT_DIR = c('report_output_dir', 'd', '1', 'character')
-
-
-spec = t(as.data.frame(spec_list))
-
-opt = getopt(spec)
-# arguments are accessed by long flag name (the first column in the spec matrix)
-#                        NOT by element name in the spec_list
-# example: opt$help, opt$expression_file
-##====== End of arguments handling ==========
-
-
-mgsub = function(pattern, replacement, x) {
-    if (length(pattern) != length(replacement)) {
-        stop("pattern and replacement have to be the same in length")
-    }
-
-    result = x
-
-    for (i in 1 : length(pattern)) {
-        result = try(gsub(pattern[i], replacement[i], x = result))
-    }
-
-    result
-}
-
-
-##====== replace variables in tpl file ======
-p = c('READS',
-'ECHO',
-'FASTQC_TPL',
-'REPORT_OUTPUT_DIR',
-'REPORT')
-r = c(opt$reads,
-opt$echo,
-opt$fastqc_tpl,
-opt$report_output_dir,
-opt$report)
-
-fastqc_report_tpl = mgsub(p, r, readLines(opt$fastqc_tpl))
-
-##====== write replaced text into Rmd file ===
-fileConn = file('fastqc_report.Rmd')
-writeLines(fastqc_report_tpl, con = fileConn)
-close(fileConn)
-
-##====== render Rmd files ====================
-rmarkdown::render('fastqc_report.Rmd')
-file.copy('fastqc_report.html', opt$report, recursive = TRUE)
-paste0('cp -r ./* ', opt$report_output_dir) %>%
-system()
-