diff bdss_client_sra.Rmd @ 22:89cc5b026494 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 8d95d985955944734cd00ac94346e1197a4feb20-dirty

--- a/bdss_client_sra.Rmd	Sat Oct 14 19:54:57 2017 -0400
+++ b/bdss_client_sra.Rmd	Sat Oct 14 22:59:06 2017 -0400
@@ -38,9 +38,9 @@
 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 != '']
+sra_ids_se = sra_ids_se[sra_ids_se != '']
 # loop through SRA accessions to download and extract reads.
-for(id in sra_ids) {
+for(id in sra_ids_se) {
     # build URL from SRA id
     url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
                  substr(id, 1, 3), '/',
@@ -50,17 +50,19 @@
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if('FORMAT' == 'fasta') {
-      command = paste0('fastq-dump --fasta -O read_files_directory ', id)
+      command = paste0('fastq-dump --fasta -O se_read_files_directory ', id, '.sra')
     } else {
-      command = paste0('fastq-dump -O read_files_directory ', id)
+      command = paste0('fastq-dump -O se_read_files_directory ', id, '.sra')
     }
+    cat('----convert SRA to fastq/fasta------\n')
+    print(system(command, intern = TRUE))
 }
 
 # download and extract reads (paired end)
 sra_ids_pe = strsplit(gsub(',', ' ', 'SRA_IDS_PE'), ' ')[[1]]
-sra_ids_pe = sra_ids[sra_ids != '']
+sra_ids_pe = sra_ids_pe[sra_ids_pe != '']
 # loop through SRA accessions to download and extract reads.
-for(id in sra_ids) {
+for(id in sra_ids_pe) {
     # build URL from SRA id
     url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
                  substr(id, 1, 3), '/',
@@ -70,14 +72,29 @@
     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)
+      command = paste0('fastq-dump --fasta --split-files -O pe_read_files_directory ', id, '.sra')
     } else {
-      command = paste0('fastq-dump --split-files -O pe_read_files_directory ', id)
+      command = paste0('fastq-dump --split-files -O pe_read_files_directory ', id, '.sra')
     }
+    cat('----convert SRA to fastq/fasta------\n')
+    command_stdout = system(command, intern = TRUE)
+    print(command_stdout)
+    if(length(command_stdout) < 3) {
+      # this is not a paired end SRA file. The corresponding file will be deleted.
+      cat(paste0(id, 'is not paired end SRA, the corresponding fastq/fasta file will deleted.'))
+      system(paste0('rm pe_read_files_directory/', id, '_1.*'), intern = TRUE)
+    }
+    
 }
 
+cat('-----single end files----\n')
+list.files('./se_read_files_directory')
+cat('-----paired end files----\n')
+list.files('./pe_read_files_directory')
+
+cat('-----Renaming files------\n')
 # rename files for paired end reads
-old_files = paste0('./read_files_directory/', list.files('./read_files_directory'))
+old_files = paste0('./pe_read_files_directory/', list.files('./pe_read_files_directory'))
 new_files = gsub('_1', '_forward', old_files)
 new_files = gsub('_2', '_reverse', new_files)
 file.rename(old_files, new_files)