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Rayan CHIKHI
serratus-batch-dl
Commits
ba287657
Commit
ba287657
authored
Jun 23, 2020
by
Rayan
Browse files
cleanup fix
parent
8a224330
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/batch_processor.py
View file @
ba287657
...
...
@@ -139,7 +139,8 @@ def process_file(accession, region):
# cleanup. #(important when using a local drive)
os
.
system
(
' '
.
join
([
"rm"
,
"-f"
,
"out/"
+
accession
+
"*.fastq"
]))
os
.
system
(
' '
.
join
([
"rm"
,
"-f"
,
accession
+
".fastq"
]))
os
.
system
(
' '
.
join
([
"rm"
,
"-f"
,
"public/sra/"
+
accession
+
".sra"
]))
os
.
system
(
' '
.
join
([
"rm"
,
"-f"
,
"public/sra/"
+
accession
+
".sra"
]))
# maybe not the right path
os
.
system
(
'rm -Rf '
+
accession
)
# seems to be the right path
endTime
=
datetime
.
now
()
diffTime
=
endTime
-
startTime
...
...
@@ -147,7 +148,6 @@ def process_file(accession, region):
sdb_log
(
sdb
,
accession
,
'batch_dl_date'
,
str
(
datetime
.
now
()))
logMessage
(
accession
,
"Serratus-batch-dl processing time - "
+
str
(
diffTime
.
seconds
),
LOGTYPE_INFO
)
def
main
():
accession
=
""
region
=
"us-east-1"
...
...
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