Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

comparison bdss_client_sra_pe.Rmd @ 7:efb1938c3020 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author mingchen0919
date Wed, 11 Oct 2017 13:21:54 -0400
parents 415ebc9016da
children fe5f30584308
comparison
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6:415ebc9016da 7:efb1938c3020
29 sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]] 29 sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]]
30 sra_accessions = sra_accessions[sra_accessions != ''] 30 sra_accessions = sra_accessions[sra_accessions != '']
31 # loop through SRA accessions to download and extract reads. 31 # loop through SRA accessions to download and extract reads.
32 for(id in sra_accessions) { 32 for(id in sra_accessions) {
33 if (SRA_BOOLEAN) { 33 if (SRA_BOOLEAN) {
34
34 # build URL from SRA accession 35 # build URL from SRA accession
35 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/', 36 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
37 substr(id, 1, 3), '/',
36 substr(id, 1, 6), '/', id, '/', id, '.sra') 38 substr(id, 1, 6), '/', id, '/', id, '.sra')
37 # download sra file with bdss 39 # download sra file with bdss
38 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url) 40 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
39 system(bdss_command, intern = TRUE) 41 system(bdss_command, intern = TRUE)
40 # convert .sra to .fastq/.fasta 42 # convert .sra to .fastq/.fasta