def _flagdownload(self): ## if download data do it and then exit. Runs single core in CLI. if len(self.args.download) == 1: downloaddir = "sra-fastqs" else: downloaddir = self.args.download[1] # call the analysis tool import ipyrad.analysis as ipa sra = ipa.sratools( accessions=self.args.download[0], workdir=downloaddir, ) # get run info and print spacer after df = sra.fetch_runinfo((1, 4, 6, 29, 30)) print("") # rename spots for prettier printing and send to screen df.rename(columns={"spots_with_mates": "mates"}, inplace=True) print(df) # run download with default name_fields and separator sra.run( name_fields=(30, 1), name_separator="_", force=self.args.force, auto=True, show_cluster=True, ) print("")
def sratools_download(SRP, workdir='SRA_fastqs', force=False): import ipyrad.analysis as ipa sra = ipa.sratools(accession=SRP, workdir=workdir) ## get run info and print spacer after df = sra.fetch_runinfo((1,4,6,29,30)) print("") ## rename spots for prettier printing and send to screen df.rename(columns={"spots_with_mates": "mates"}, inplace=True) print(df) ## run download with default name_fields and separator sra.run(name_fields=(30, 1), name_separator="_", force=force) print("")