Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

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author mingchen0919
date Tue, 17 Oct 2017 14:09:01 -0400
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512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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1 ---
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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2 title: 'Download and extract single end fastq/fasta data with BDSS client from SRA accessions'
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3 output:
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4 html_document:
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5 number_sections: true
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6 toc: true
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7 theme: cosmo
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8 highlight: tango
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9 ---
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10
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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12 knitr::opts_chunk$set(
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13 echo = ECHO,
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14 error=TRUE
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15 )
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16 ```
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18 # Command line arguments
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20 ```{r 'command line arguments'}
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21 str(opt)
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mingchen0919
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22 ```
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24 # BDSS configuration file
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25
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mingchen0919
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26 First, we create a bdss configuration file `bdss.cfg` in the current directory.
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27
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mingchen0919
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28 ```{r}
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29 system('echo "[metadata_repository]" > bdss.cfg')
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30 system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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31 ```
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32
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33 # Download and extract reads
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34
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35 ```{r 'download and extract reads'}
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mingchen0919
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36 # create two directories, one for single end and the other for paired end SRA reads.
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mingchen0919
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37 dir.create('se_read_files_directory')
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38 dir.create('pe_read_files_directory')
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mingchen0919
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39 # download and extract reads (single end)
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40 sra_ids_se = strsplit(gsub(',', ' ', 'SRA_IDS_SE'), ' ')[[1]]
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mingchen0919
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41 sra_ids_se = sra_ids_se[sra_ids_se != '']
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mingchen0919
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42 # loop through SRA accessions to download and extract reads.
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43 for(id in sra_ids_se) {
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44 # build URL from SRA id
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45 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
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46 substr(id, 1, 3), '/',
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47 substr(id, 1, 6), '/', id, '/', id, '.sra')
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48 # download sra file with bdss
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49 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
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50 system(bdss_command, intern = TRUE)
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51 # convert .sra to .fastq/.fasta
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52 if('FORMAT' == 'fasta') {
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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53 command = paste0('fastq-dump --fasta -O se_read_files_directory ', id, '.sra')
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54 } else {
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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55 command = paste0('fastq-dump -O se_read_files_directory ', id, '.sra')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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56 }
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57 cat('----convert SRA to fastq/fasta------\n')
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58 print(system(command, intern = TRUE))
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59 }
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60
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61 # download and extract reads (paired end)
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62 sra_ids_pe = strsplit(gsub(',', ' ', 'SRA_IDS_PE'), ' ')[[1]]
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63 sra_ids_pe = sra_ids_pe[sra_ids_pe != '']
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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64 # loop through SRA accessions to download and extract reads.
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65 for(id in sra_ids_pe) {
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66 # build URL from SRA id
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67 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
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68 substr(id, 1, 3), '/',
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69 substr(id, 1, 6), '/', id, '/', id, '.sra')
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70 # download sra file with bdss
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71 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
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72 system(bdss_command, intern = TRUE)
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73 # convert .sra to .fastq/.fasta
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mingchen0919
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74 if('FORMAT' == 'fasta') {
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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75 command = paste0('fastq-dump --fasta --split-files -O pe_read_files_directory ', id, '.sra')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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76 } else {
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mingchen0919
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77 command = paste0('fastq-dump --split-files -O pe_read_files_directory ', id, '.sra')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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78 }
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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79 cat('----convert SRA to fastq/fasta------\n')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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80 command_stdout = system(command, intern = TRUE)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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81 print(command_stdout)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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82 if(!(paste0(id, '_2.FORMAT') %in% list.files('pe_read_files_directory'))) {
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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83 # this is not a paired end SRA file. The corresponding file will be deleted.
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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84 cat(paste0(id, ' is not paired end SRA, the corresponding fastq/fasta file will deleted.'))
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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85 system(paste0('rm pe_read_files_directory/', id, '_1.*'), intern = TRUE)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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86 }
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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87
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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88 }
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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89
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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90 cat('-----single end files----\n')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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91 list.files('./se_read_files_directory')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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92 cat('-----paired end files----\n')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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93 list.files('./pe_read_files_directory')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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94
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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95 cat('-----Renaming files------\n')
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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96 # rename files for paired end reads
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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97 old_files = paste0('./pe_read_files_directory/', list.files('./pe_read_files_directory'))
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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98 print(old_files)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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99 new_files = gsub('_1', '_forward', old_files)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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100 new_files = gsub('_2', '_reverse', new_files)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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101 print(new_files)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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102 file.rename(old_files, new_files)
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
parents:
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103 ```
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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104
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
parents:
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105