Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

annotate fastq_dump_pe.Rmd @ 12:d330ce2d4663 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
author mingchen0919
date Wed, 27 Sep 2017 16:49:22 -0400
parents d4a9c31d0046
children 66bc1016ec2a
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mingchen0919
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1 ---
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mingchen0919
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2 title: 'Fastq-dump: download and extract paired end reads into FASTQ/FASTA file'
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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3 output:
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mingchen0919
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4 html_document:
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mingchen0919
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5 number_sections: true
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mingchen0919
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6 toc: true
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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7 theme: cosmo
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mingchen0919
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8 highlight: tango
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mingchen0919
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9 ---
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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10
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mingchen0919
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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12 knitr::opts_chunk$set(
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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13 echo = ECHO
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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14 )
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15 ```
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d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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17 # Command line arguments
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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mingchen0919
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19 ```{r 'command line arguments'}
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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20 str(opt)
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mingchen0919
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21 ```
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mingchen0919
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23 # Download and extract reads
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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mingchen0919
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25 ```{r 'download and extract reads'}
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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26 # create a directory to store read files
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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27 dir.create('read_files_directory')
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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28 # download and extract reads
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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29 sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]]
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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30 sra_accessions = sra_accessions[sra_accessions != '']
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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31 # loop through SRA accessions to download and extract reads.
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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32 for(id in sra_accessions) {
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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33 if('FORMAT' == 'fasta') {
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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34 command = paste0('fastq-dump --fasta ', '-O read_files_directory ')
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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35 } else {
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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36 command = paste0('fastq-dump ', '-O read_files_directory ')
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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37 }
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39 if('SPLIT_FILES' == TRUE) {
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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40 command = paste0(command, '--split_files ', id)
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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41 } else {
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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42 command = paste0(command, id)
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43 }
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44 print(command)
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45 system(command = command)
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46 }
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47 ```
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48
12
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49 # Rename files
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51 ```{r}
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52 old_files = paste0('./read_files_directory/', list.files('./read_files_directory'))
d330ce2d4663 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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53 new_files = gsub('_1', '_forward', old_files)
d330ce2d4663 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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54 new_files = gsub('_2', '_reverse', new_files)
d330ce2d4663 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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55 file.copy('./read_files_directory/')
d330ce2d4663 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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56 ```
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