view bdss_client_sra.Rmd @ 21:a709a705ce09 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty

---
title: 'Download and extract single end fastq/fasta data with BDSS client from SRA accessions'
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,
  error=TRUE
)
```

# Command line arguments

```{r 'command line arguments'}
str(opt)
```

# BDSS configuration file

First, we create a bdss configuration file `bdss.cfg` in the current directory.

```{r}
system('echo "[metadata_repository]" > bdss.cfg')
system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
```

# Download and extract reads

```{r 'download and extract reads'}
# create two directories, one for single end and the other for paired end SRA reads.
dir.create('se_read_files_directory')
dir.create('pe_read_files_directory')
# download and extract reads (single end)
sra_ids_se = strsplit(gsub(',', ' ', 'SRA_IDS_SE'), ' ')[[1]]
sra_ids_se = sra_ids[sra_ids != '']
# loop through SRA accessions to download and extract reads.
for(id in sra_ids) {
    # build URL from SRA id
    url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
                 substr(id, 1, 3), '/',
                 substr(id, 1, 6), '/', id, '/', id, '.sra')
    # download sra file with bdss
    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
    system(bdss_command, intern = TRUE)
    # convert .sra to .fastq/.fasta
    if('FORMAT' == 'fasta') {
      command = paste0('fastq-dump --fasta -O read_files_directory ', id)
    } else {
      command = paste0('fastq-dump -O read_files_directory ', id)
    }
}

# download and extract reads (paired end)
sra_ids_pe = strsplit(gsub(',', ' ', 'SRA_IDS_PE'), ' ')[[1]]
sra_ids_pe = sra_ids[sra_ids != '']
# loop through SRA accessions to download and extract reads.
for(id in sra_ids) {
    # build URL from SRA id
    url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
                 substr(id, 1, 3), '/',
                 substr(id, 1, 6), '/', id, '/', id, '.sra')
    # download sra file with bdss
    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
    system(bdss_command, intern = TRUE)
    # convert .sra to .fastq/.fasta
    if('FORMAT' == 'fasta') {
      command = paste0('fastq-dump --fasta --split-files -O pe_read_files_directory ', id)
    } else {
      command = paste0('fastq-dump --split-files -O pe_read_files_directory ', id)
    }
}

# rename files for paired end reads
old_files = paste0('./read_files_directory/', list.files('./read_files_directory'))
new_files = gsub('_1', '_forward', old_files)
new_files = gsub('_2', '_reverse', new_files)
file.rename(old_files, new_files)
```