Mercurial > repos > mingchen0919 > aurora_bdss_sra
changeset 10:4b73dbd97a0e draft default tip
planemo upload for repository https://github.com/feltus/BDSS
| author | mingchen0919 |
|---|---|
| date | Tue, 12 Jun 2018 12:30:21 -0400 |
| parents | 39831b70aabb |
| children | |
| files | rmarkdown_report.Rmd |
| diffstat | 1 files changed, 5 insertions(+), 9 deletions(-) [+] |
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--- a/rmarkdown_report.Rmd Tue Jun 12 12:12:56 2018 -0400 +++ b/rmarkdown_report.Rmd Tue Jun 12 12:30:21 2018 -0400 @@ -76,7 +76,6 @@ # download sra file with bdss bdss_command = paste0('bdss transfer -u ', url, '>> ${REPORT_FILES_PATH}/log.txt 2>&1') command_stdout = system(bdss_command, intern = TRUE) - write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE) # convert .sra to .fastq/.fasta if(opt$X_f == 'fasta') { command = paste0('fastq-dump --fasta -O ', se_dir, ' ', id, '.sra') @@ -99,7 +98,6 @@ # download sra file with bdss bdss_command = paste0('bdss transfer -u ', url, '>> ${REPORT_FILES_PATH}/log.txt 2>&1') command_stdout = system(bdss_command, intern = TRUE) - write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE) # convert .sra to .fastq/.fasta if(opt$X_f == 'fasta') { command = paste0('fastq-dump --fasta --split-files -O ', pe_dir, ' ', id, '.sra') @@ -108,17 +106,15 @@ } command_stdout = system(command, intern = TRUE) write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE) - # if(!(paste0(id, '_2.', opt$X_f) %in% list.files('pe_read_files_dir'))) { - # # 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.')) - # command_stdout = system(paste0('rm ', pe_dir, '/', id, '_1.*'), intern = TRUE) - # } - } +``` + +```{r echo=FALSE} # rename files for paired end reads old_files = list.files(path = pe_dir, full.names = TRUE) new_files = gsub('_1', '_forward', old_files) new_files = gsub('_2', '_reverse', new_files) -file.rename(old_files, new_files) +res = file.rename(old_files, new_files) ``` +