encode_downloader.py creates multiple unnecessary directories

[stolarczyk]

empty dir

[mjs5kd@udc-ba36-36 new](master): ll
total 8.0K
drwxrwxr-x 2 mjs5kd users    0 Nov 18 13:01 .
drwxrwxr-x 3 mjs5kd users 4.5K Nov 18 12:55 ..

encode_downloader.py run

[mjs5kd@udc-ba36-36 new](master): python3.6 "https://www.encodeproject.org/experiments/ENCSR611JJS" --file-types bed --assemblies hg19
['ENCSR611JJS']
========== ENCSR611JJS ==========
assembly: GRCh38
Downloading (bed): https://www.encodeproject.org/files/ENCFF455ZJN/@@download/ENCFF455ZJN.bed.gz, rep:[1], pair:-1
Continuing in background, pid 120900.
Downloading (bed): https://www.encodeproject.org/files/ENCFF317YVO/@@download/ENCFF317YVO.bed.gz, rep:[1, 2], pair:-1
Continuing in background, pid 120908.
Downloading (bed): https://www.encodeproject.org/files/ENCFF947IJX/@@download/ENCFF947IJX.bed.gz, rep:[1, 2], pair:-1
Continuing in background, pid 120916.
Downloading (bed): https://www.encodeproject.org/files/ENCFF799ZCH/@@download/ENCFF799ZCH.bed.gz, rep:[2], pair:-1
Continuing in background, pid 120925.

result

[mjs5kd@udc-ba36-36 new](master): ll
total 48K
drwxrwxr-x 11 mjs5kd users 5.0K Nov 18 13:01 .
drwxrwxr-x  3 mjs5kd users 4.5K Nov 18 12:55 ..
-rw-rw-r--  1 mjs5kd users 1.3K Nov 18 13:01 all_files.tsv
drwxrwxr-x  2 mjs5kd users    0 Nov 18 13:01 and
drwxrwxr-x  2 mjs5kd users    0 Nov 18 13:01 as
drwxrwxr-x  2 mjs5kd users    0 Nov 18 13:01 background
drwxrwxr-x  3 mjs5kd users 1.5K Nov 18 13:01 ENCSR611JJS
drwxrwxr-x  2 mjs5kd users    0 Nov 18 13:01 for
drwxrwxr-x  3 mjs5kd users  512 Nov 18 13:01 idr
drwxrwxr-x  2 mjs5kd users    0 Nov 18 13:01 input
drwxrwxr-x  3 mjs5kd users  512 Nov 18 13:01 peaks
drwxrwxr-x  2 mjs5kd users    0 Nov 18 13:01 thresholded

[leepc12]

Fixed