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("")