Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

annotate fastq_dump_se.Rmd @ 0:7ec600e7dba7 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_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
author mingchen0919
date Wed, 27 Sep 2017 09:25:48 -0400
parents
children 4c84d748da08
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
1 ---
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
3 output:
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
4 html_document:
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
6 toc: true
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
7 theme: cosmo
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
8 highlight: tango
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
9 ---
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
10
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
13 echo = ECHO
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
14 )
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
15 ```
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
16
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
18
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
20 str(opt)
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
21 ```
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
22
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
24
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
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
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
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
mingchen0919
parents:
diff changeset
32 for(id in sra_accessions) {
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
33 if(FORMAT == 'fasta') {
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
34 command = paste0('fastq-dump --fasta ', id, ' -O 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
parents:
diff changeset
35 } else {
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
36 command = paste0('fastq-dump ', id, ' -O 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
parents:
diff changeset
37 }
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
38 system(command = command)
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
39 }
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
40 ```
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
parents:
diff changeset
41