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1 ---
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2 title: 'FASTA splitter'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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7
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8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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9 knitr::opts_chunk$set(echo = TRUE, error = TRUE)
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10 ```
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11
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12
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13 ```{bash}
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14 # build job-script
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15 mkdir -p ${WORKING_DIR}/fasta_files
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16
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17 # single-end.sh
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18 cat <<EOF >${X_d}/job-script.sh
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19 cd ${WORKING_DIR}/fasta_files && \\
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20 cp ${X_A} input.fasta && \\
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21 ${X_t}/split.pl input.fasta ${X_B} > ${X_d}/fasta_splitter-log.txt 2>&1
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22 EOF
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23 ```
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24
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25 ```{bash, 'run jobs', echo=FALSE}
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26 # run job script, always use absolute path.
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27 # we want to run all jobs within the working path.
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28 sh ${X_d}/job-script.sh
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29 ```
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30
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2
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31 ```{bash}
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32 # remove original input fasta
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33 rm ${WORKING_DIR}/fasta_files/input.fasta
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34 mv ${WORKING_DIR}/fasta_files/out ${X_d}/split-out.txt
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35 ```
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36
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37 ```{r, 'display output directory contents', results='asis', echo=FALSE}
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38 ## after the job is done, we list all files from the output directory.
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39 ## full relative path to the output directory needs to be displayed.
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40
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41 cat('##All output files')
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42 cat('\n\n')
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43 all_files = list.files(path = opt$X_d,
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44 full.names = TRUE,
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45 recursive = TRUE)
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46
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47 for (f in sub(opt$X_d, '.', all_files) ) {
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48 cat('* [', f, '](', f, ')\n')
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49 }
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50 cat('\n')
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51 ```
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52
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