Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

diff 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
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line diff
--- a/bdss_client_sra_pe.Rmd	Wed Oct 11 11:49:19 2017 -0400
+++ b/bdss_client_sra_pe.Rmd	Wed Oct 11 13:21:54 2017 -0400
@@ -31,8 +31,10 @@
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
   if (SRA_BOOLEAN) {
+    
     # build URL from SRA accession
-    url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/',
+    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)