Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

annotate fastq_dump_se.Rmd @ 17:cf1233051a9b draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit e6035405141d63626702084eacd02089f816cdc7-dirty
author mingchen0919
date Wed, 27 Sep 2017 17:12:39 -0400
parents d4a9c31d0046
children 42e154ba2d35
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
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1 ---
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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2 title: 'Fastq-dump: download and extract single end reads into FASTQ/FASTA file'
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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3 output:
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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4 html_document:
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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5 number_sections: true
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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6 toc: true
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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7 theme: cosmo
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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8 highlight: tango
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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9 ---
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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12 knitr::opts_chunk$set(
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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13 echo = ECHO
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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14 )
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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15 ```
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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17 # Command line arguments
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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19 ```{r 'command line arguments'}
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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20 str(opt)
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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21 ```
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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23 # Download and extract reads
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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25 ```{r 'download and extract reads'}
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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26 # create a directory to store read files
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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27 dir.create('read_files_directory')
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
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28 # download and extract reads
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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29 sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]]
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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30 sra_accessions = sra_accessions[sra_accessions != '']
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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31 # loop through SRA accessions to download and extract reads.
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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32 for(id in sra_accessions) {
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33 if('FORMAT' == 'fasta') {
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34 command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id)
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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35 } else {
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36 command = paste0('fastq-dump ', '-O read_files_directory ', id)
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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37 }
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38 print(command)
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39 system(command = command)
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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40 }
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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41 ```
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