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Change os.rename for shutil.move #9

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Change os.rename for shutil.move #9

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10 changes: 5 additions & 5 deletions download.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
import functools
import time
import subprocess
from shutil import move as shutil_move
from shutil import copy as shutil_copy


def get_read_run_info(ena_id):
Expand Down Expand Up @@ -126,14 +128,12 @@ def download_with_sra_prefetch(aspera_key, outdir, pickle_prefix, ena_id):
_, prefetch_outdir, _ = utils.runCommandPopenCommunicate(['echo', '$HOME/ncbi/public/sra'], True, None, False)

try:
os.rename(os.path.join(prefetch_outdir.splitlines()[0], ena_id + '.sra'),
os.path.join(outdir, ena_id + '.sra'))
shutil_move(os.path.join(prefetch_outdir.splitlines()[0], ena_id + '.sra'),
os.path.join(outdir, ena_id + '.sra'))
except OSError as e:
print('Found the following error:'
'{}'.format(e))

from shutil import copy as shutil_copy

shutil_copy(os.path.join(prefetch_outdir.splitlines()[0], ena_id + '.sra'),
os.path.join(outdir, ena_id + '.sra'))
os.remove(os.path.join(prefetch_outdir.splitlines()[0], ena_id + '.sra'))
Expand Down Expand Up @@ -476,7 +476,7 @@ def rename_move_files(list_files, new_name, outdir, download_paired_type):
if os.path.isfile(list_files[i]):
os.remove(list_files[i])
else:
os.rename(list_files[i], list_new_files[i])
shutil_move(list_files[i], list_new_files[i])
list_new_files = list_new_files.values()
except Exception as e:
print(e)
Expand Down