def mirror_sample(sample_accession):
import ena
filetable = ena.get_project_reads_table(sample_accession,
as_pandas_DataFrame=True)
filetable = ena.expand_fastq_columns(filetable)
mirror_all_files(study_accession, filetable, MIRROR_BASEDIR, use=DL_METHOD)
return filetable
def create_mirror(study_accession, target_directory):
import ena
filetable = ena.get_project_reads_table(study_accession, as_pandas_DataFrame=True)
filetable = ena.expand_fastq_columns(filetable)
mirror_all_files(filetable, MIRROR_BASEDIR, use_aspera=USE_ASPERA)
if target_directory != '*':
build_link_structure(filetable, MIRROR_BASEDIR, target_directory, study_accession)
return filetable
def create_mirror(study_accession, target_directory):
import ena
filetable = ena.get_project_reads_table(study_accession, as_pandas_DataFrame=True)
filetable = ena.expand_fastq_columns(filetable)
mirror_all_files(filetable, MIRROR_BASEDIR, use_aspera=USE_ASPERA)
if target_directory != '*':
try:
build_link_structure(filetable, MIRROR_BASEDIR, target_directory, study_accession)
except IndexError:
print("Failed to create link structure for:", study_accession, file=sys.stderr)
raise
return filetable
def mirror_sample(sample_accession):
import ena
filetable = ena.get_project_reads_table(sample_accession, as_pandas_DataFrame=True)
filetable = ena.expand_fastq_columns(filetable)
mirror_all_files(filetable, MIRROR_BASEDIR, use_aspera=USE_ASPERA)
return filetable