Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site

annotate 01_evaluation_overview.Rmd @ 5:0ac073bef19d draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
author mingchen0919
date Tue, 08 Aug 2017 11:45:41 -0400
parents d732d4526c6d
children 507eec497730
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d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
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1 ---
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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2 title: "Evaluation Overview"
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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3 output: html_document
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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4 ---
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5
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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7 knitr::opts_chunk$set(echo = ECHO)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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8 ```
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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9
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10 ```{bash 'copy data from datasets directory to working directory', echo=FALSE}
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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11 # Copy uploaded data to the working directory
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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12 for f in $(echo READS | sed "s/,/ /g")
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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13 do
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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14 cp $f ./
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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15 done
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16 ```
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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17
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18 ```{bash 'run fastqc', echo=FALSE}
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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19 # run fastqc and place outputs into the report directory
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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20 for r in $(ls *.dat)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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21 do
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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22 fastqc -o REPORT_OUTPUT_DIR $r > /dev/null 2>&1
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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23 done
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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24 ```
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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26 ```{bash 'parse fastqc results', echo=FALSE}
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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27 ##==== copy fastqc generated zip files from report output directory to job work directory ==
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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28 cp -r REPORT_OUTPUT_DIR/*zip ./
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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30 # create a file to store data file paths
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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31 echo "sample_id,file_path" > PWF_file_paths.txt # Pass, Warning, Fail
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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32 echo "sample_id,file_path" > PBQS_file_paths.txt # Per Base Quality Score
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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33 echo "sample_id,file_path" > PSQS_file_paths.txt # Per Sequence Quality Score
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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34 echo "sample_id,file_path" > PSGC_file_paths.txt # Per Sequence GC Content
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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35 echo "sample_id,file_path" > PBSC_file_paths.txt # Per Base Sequence Content
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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36 echo "sample_id,file_path" > PBNC_file_paths.txt # Per Base N Content
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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37 echo "sample_id,file_path" > SDL_file_paths.txt # Sequence Duplication Level
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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38 echo "sample_id,file_path" > SLD_file_paths.txt # Sequence Length Distribution
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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39 echo "sample_id,file_path" > KMC_file_paths.txt # Kmer Content
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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41 for i in $(ls *.zip)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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42 do
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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43 BASE=$(echo $i | sed 's/\(.*\)\.zip/\1/g')
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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44 echo $BASE
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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45 unzip ${BASE}.zip > /dev/null 2>&1
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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46
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47 ##====== pass,warning,fail (WSF) =============
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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48 awk '/^>>/ {print}' "$BASE"/fastqc_data.txt | grep -v 'END_MODULE' | sed 's/>>//' > "$BASE"-PWF.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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49 echo "${BASE},${BASE}-PWF.txt" >> PWF_file_paths.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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51 ##====== per base quality scores (PBQS) ======
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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52 awk '/^>>Per base sequence quality/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBQS.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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53 echo "${BASE},${BASE}-PBQS.txt" >> PBQS_file_paths.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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54
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55 ##====== per sequence quality scores (PSQS)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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56 awk '/^>>Per sequence quality scores/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSQS.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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57 echo "${BASE},${BASE}-PSQS.txt" >> PSQS_file_paths.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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58
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59 ##====== Per sequence GC content (PSGC)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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60 awk '/^>>Per sequence GC content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSGC.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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61 echo "${BASE},${BASE}-PSGC.txt" >> PSGC_file_paths.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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63 ##====== Per Base Sequence Content (PBSC)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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64 awk '/^>>Per base sequence content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBSC.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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65 echo "${BASE},${BASE}-PBSC.txt" >> PBSC_file_paths.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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67 ##====== Per Base N Content (PBNC)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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68 awk '/^>>Per base N content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBNC.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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69 echo "${BASE},${BASE}-PBNC.txt" >> PBNC_file_paths.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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71 ##====== Sequence Duplication Level (SDL)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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72 awk '/^>>Sequence Duplication Levels/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SDL.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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73 echo "${BASE},${BASE}-SDL.txt" >> SDL_file_paths.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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75 ##====== Sequence Length Distribution (SLD)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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76 awk '/^>>Sequence Length Distribution/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SLD.txt
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
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77 echo "${BASE},${BASE}-SLD.txt" >> SLD_file_paths.txt
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78
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79 ##====== Kmer Content ============
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80 awk '/^>>Kmer Content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-KMC.txt
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81 echo "${BASE},${BASE}-KMC.txt" >> KMC_file_paths.txt
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82
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83 done
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84 ```
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85
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86
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87 ## Evaluation Overview
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88
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89 ```{r 'overview'}
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90 PWF_file_paths = read.csv('PWF_file_paths.txt',
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91 header = TRUE, stringsAsFactors = FALSE)
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92 rm('PWF_df')
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93 for(i in 1:nrow(PWF_file_paths)) {
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94 file_path = PWF_file_paths[i,2]
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95 pwf_df = read.csv(file_path,
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96 sep='\t', header=FALSE, stringsAsFactors = FALSE)
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97 colnames(pwf_df) = c('item', PWF_file_paths[i,1])
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98 if (!exists('PWF_df')) {
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99 PWF_df = pwf_df
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100 } else {
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101 PWF_df = cbind(PWF_df, pwf_df[,2,drop=FALSE])
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102 }
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103 }
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104 ```
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105
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106
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107 ```{r}
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108 my_icon = c('ok', 'remove', 'star')
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109 names(my_icon) = c('pass', 'fail', 'warn')
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110 evaluate_list = list()
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111 for (i in colnames(PWF_df)[-1]) {
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112 evaluate_list[[i]] = formatter(
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113 "span",
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114 style = x ~ style("background-color" = ifelse(x =='pass', '#9CD027', ifelse(x == 'fail', '#CC0000', '#FF4E00')),
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115 "color" = "white",
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116 "width" = "50px",
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117 "float" = "left",
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118 "padding-right" = "5px")
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119 )
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120 }
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121
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122 formattable(PWF_df, evaluate_list)
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123 ```