Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

annotate bdss_client_sra.Rmd @ 21:a709a705ce09 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
author mingchen0919
date Sat, 14 Oct 2017 19:54:57 -0400
parents
children 89cc5b026494
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
21
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
1 ---
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
2 title: 'Download and extract single end fastq/fasta data with BDSS client from SRA accessions'
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
3 output:
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
4 html_document:
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
5 number_sections: true
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
6 toc: true
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
7 theme: cosmo
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
8 highlight: tango
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
9 ---
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
10
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
12 knitr::opts_chunk$set(
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
13 echo = ECHO,
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
14 error=TRUE
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
15 )
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
16 ```
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
17
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
18 # Command line arguments
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
19
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
20 ```{r 'command line arguments'}
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
21 str(opt)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
22 ```
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
23
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
24 # BDSS configuration file
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
25
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
26 First, we create a bdss configuration file `bdss.cfg` in the current directory.
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
27
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
28 ```{r}
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
29 system('echo "[metadata_repository]" > bdss.cfg')
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
30 system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
31 ```
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
32
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
33 # Download and extract reads
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
34
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
35 ```{r 'download and extract reads'}
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
36 # create two directories, one for single end and the other for paired end SRA reads.
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
37 dir.create('se_read_files_directory')
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
38 dir.create('pe_read_files_directory')
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
39 # download and extract reads (single end)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
40 sra_ids_se = strsplit(gsub(',', ' ', 'SRA_IDS_SE'), ' ')[[1]]
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
41 sra_ids_se = sra_ids[sra_ids != '']
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
42 # loop through SRA accessions to download and extract reads.
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
43 for(id in sra_ids) {
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
44 # build URL from SRA id
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
45 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
46 substr(id, 1, 3), '/',
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
47 substr(id, 1, 6), '/', id, '/', id, '.sra')
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
48 # download sra file with bdss
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
49 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
50 system(bdss_command, intern = TRUE)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
51 # convert .sra to .fastq/.fasta
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
52 if('FORMAT' == 'fasta') {
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
53 command = paste0('fastq-dump --fasta -O read_files_directory ', id)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
54 } else {
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
55 command = paste0('fastq-dump -O read_files_directory ', id)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
56 }
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
57 }
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
58
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
59 # download and extract reads (paired end)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
60 sra_ids_pe = strsplit(gsub(',', ' ', 'SRA_IDS_PE'), ' ')[[1]]
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
61 sra_ids_pe = sra_ids[sra_ids != '']
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
62 # loop through SRA accessions to download and extract reads.
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
63 for(id in sra_ids) {
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
64 # build URL from SRA id
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
65 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
66 substr(id, 1, 3), '/',
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
67 substr(id, 1, 6), '/', id, '/', id, '.sra')
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
68 # download sra file with bdss
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
69 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
70 system(bdss_command, intern = TRUE)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
71 # convert .sra to .fastq/.fasta
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
72 if('FORMAT' == 'fasta') {
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
73 command = paste0('fastq-dump --fasta --split-files -O pe_read_files_directory ', id)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
74 } else {
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
75 command = paste0('fastq-dump --split-files -O pe_read_files_directory ', id)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
76 }
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
77 }
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
78
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
79 # rename files for paired end reads
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
80 old_files = paste0('./read_files_directory/', list.files('./read_files_directory'))
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
81 new_files = gsub('_1', '_forward', old_files)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
82 new_files = gsub('_2', '_reverse', new_files)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
83 file.rename(old_files, new_files)
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
84 ```
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
85
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
mingchen0919
parents:
diff changeset
86