#to grab sequences for a SRA project ID, using 24 threads and saving data and metadata
# the -o option will create the directory if it doesn't already exist
grabseqs sra -t 24 -m metadata.csv -o proj/ -r 3 PRJN#######
usage: grabseqs [-h] [--version] {sra,imicrobe,mgrast} ...
Download metagenomic sequences from public datasets.
positional arguments:
{sra,imicrobe,mgrast}
repositories available
sra download from SRA
imicrobe download from iMicrobe
mgrast download from MG-RAST
optional arguments:
-h, --help show this help message and exit
-m METADATA filename in which to save SRA metadata (.csv format,
relative to OUTDIR)
-o OUTDIR directory in which to save output. created if it doesn't
exist
-r RETRIES number of times to retry download
-t THREADS threads to use (for fasterq-dump/pigz)
-f force re-download of files
-l list (but do not download) samples to be grabbed
--parse_run_ids parse SRR/ERR identifers (do not pass straight to fasterq-
dump)
--custom_fqdump_args CUSTOM_FQD_ARGS
"string" containing args to pass to fastq-dump
--use_fastq_dump use legacy fastq-dump instead of fasterq-dump (no
multithreaded downloading)