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Rayan CHIKHI
serratus-batch-dl
Commits
9e112f17
Commit
9e112f17
authored
Jun 16, 2020
by
Rayan CHIKHI
Browse files
fixed paths
parent
1e21f696
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/batch_processor.py
View file @
9e112f17
...
...
@@ -40,7 +40,7 @@ def process_file(accession, region):
# download reads from accession
os
.
system
(
'mkdir -p out/'
)
os
.
system
(
'prefetch '
+
accession
)
os
.
system
(
'
..
/parallel-fastq-dump --split-files --outdir out/ --threads 4 --sra-id '
+
accession
)
os
.
system
(
'/parallel-fastq-dump --split-files --outdir out/ --threads 4 --sra-id '
+
accession
)
files
=
os
.
listdir
(
os
.
getcwd
()
+
"/out/"
)
print
(
"after fastq-dump, dir listing"
,
files
)
...
...
@@ -54,7 +54,7 @@ def process_file(accession, region):
# as per https://github.com/ababaian/serratus/blob/master/containers/serratus-dl/run_dl-sra.sh#L26
# run fastp
os
.
system
(
' '
.
join
([
"cat"
,
"out/*.fastq"
,
"|"
,
"
..
/fastp"
,
"--trim_poly_x"
,
"--stdin"
,
"-o"
,
accession
+
".fastq"
]))
os
.
system
(
' '
.
join
([
"cat"
,
"out/*.fastq"
,
"|"
,
"/fastp"
,
"--trim_poly_x"
,
"--stdin"
,
"-o"
,
accession
+
".fastq"
]))
if
os
.
stat
(
accession
+
".fastq"
).
st_size
==
0
:
print
(
"fastp produced empty output"
)
...
...
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