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nlecouvr
nextflow
Commits
0a73bd21
Commit
0a73bd21
authored
Feb 16, 2022
by
nlecouvr
Browse files
Update GATC_finder.py
parent
2a820420
Changes
1
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Inline
Side-by-side
src/.docker_modules/GATC_finder/script/GATC_finder.py
View file @
0a73bd21
...
...
@@ -2,15 +2,14 @@ import sys
import
re
from
Bio
import
SeqIO
if
len
(
sys
.
argv
)
<
3
:
raise
IndexError
(
"Please enter 2 arguments"
)
print
(
"test"
)
# Gets the arguments in the command line
out_file_path
=
str
(
sys
.
argv
[
2
])
out_file_path
=
"/GATC_finder"
genome_file
=
str
(
sys
.
argv
[
1
])
# Opening the file to write the positions in
f
=
open
(
out_file_path
,
"w"
)
f
=
open
(
"sites.bed"
,
"w"
)
# Motif we are looking for
motif
=
"GATC"
...
...
@@ -29,4 +28,4 @@ for seq_record in SeqIO.parse(genome_file, "fasta"):
# Writes the position in the .bed file (chro/start/end)
line
=
f
"
{
chrom
}
\t
{
start_pos
}
\t
{
end_pos
}
\n
"
f
.
write
(
line
)
\ No newline at end of file
f
.
write
(
line
)
Write
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