Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
diff fastq_dump_se.Rmd @ 0:1a11c4fd13d0 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
author | mingchen0919 |
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date | Wed, 27 Sep 2017 21:41:29 -0400 |
parents | |
children | 58d48d1157ed |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_dump_se.Rmd Wed Sep 27 21:41:29 2017 -0400 @@ -0,0 +1,51 @@ +--- +title: 'Fastq-dump: download and extract single end reads into FASTQ/FASTA file' +output: + html_document: + number_sections: true + toc: true + theme: cosmo + highlight: tango +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set( + echo = ECHO +) +``` + +# Command line arguments + +```{r 'command line arguments'} +str(opt) +``` + +# Download and extract reads + +```{r 'download and extract reads'} +# create a directory to store read files +dir.create('read_files_directory') +# download and extract reads +sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]] +sra_accessions = sra_accessions[sra_accessions != ''] +# loop through SRA accessions to download and extract reads. +for(id in sra_accessions) { + if('FORMAT' == 'fasta') { + command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id) + } else { + command = paste0('fastq-dump ', '-O read_files_directory ', id) + } +} +``` + +* `fastq-dump` command +```{r} +print(command) +``` + +* `command line stdout` + +```{r} +system(command = command, intern = TRUE) +``` +