Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
comparison fastq_dump_pe.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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-1:000000000000 | 0:1a11c4fd13d0 |
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1 --- | |
2 title: 'Fastq-dump: download and extract paired end reads into FASTQ/FASTA file' | |
3 output: | |
4 html_document: | |
5 number_sections: true | |
6 toc: true | |
7 theme: cosmo | |
8 highlight: tango | |
9 --- | |
10 | |
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
12 knitr::opts_chunk$set( | |
13 echo = ECHO | |
14 ) | |
15 ``` | |
16 | |
17 # Command line arguments | |
18 | |
19 ```{r 'command line arguments'} | |
20 str(opt) | |
21 ``` | |
22 | |
23 # Download and extract reads | |
24 | |
25 ```{r 'download and extract reads'} | |
26 # create a directory to store read files | |
27 dir.create('read_files_directory') | |
28 # download and extract reads | |
29 sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]] | |
30 sra_accessions = sra_accessions[sra_accessions != ''] | |
31 # loop through SRA accessions to download and extract reads. | |
32 for(id in sra_accessions) { | |
33 if('FORMAT' == 'fasta') { | |
34 command = paste0('fastq-dump --fasta --split-files ', '-O read_files_directory ', id) | |
35 } else { | |
36 command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id) | |
37 } | |
38 # fastq-dump command | |
39 print(command) | |
40 # command line stdout | |
41 system(command = command, intern = TRUE) | |
42 } | |
43 ``` | |
44 | |
45 | |
46 # Rename files | |
47 | |
48 ```{r} | |
49 old_files = paste0('./read_files_directory/', list.files('./read_files_directory')) | |
50 new_files = gsub('_1', '_forward', old_files) | |
51 new_files = gsub('_2', '_reverse', new_files) | |
52 file.rename(old_files, new_files) | |
53 ``` | |
54 |