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Anne-Sophie Denommé-Pichon
STR
Commits
b2154f22
Commit
b2154f22
authored
Jun 21, 2020
by
Anne-Sophie Denommé-Pichon
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Ignore empty lines in sample.list
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3 changed files
with
9 additions
and
5 deletions
+9
-5
README.md
README.md
+1
-1
getResults.py
getResults.py
+4
-2
str_outliers.py
str_outliers.py
+4
-2
No files found.
README.md
View file @
b2154f22
...
...
@@ -6,7 +6,7 @@
-
Licence: AGPLv3
-
Description: How to launch scripts to get STR genotype from genomes on all the locus tested
1.
Create
`samples.list`
1.
Create
`samples.list`
(bam file names without .bam)
2.
Fill the configuration file
`config.sh`
.
3.
Launch
`launch_pipeline.sh`
:
`nohup ./launch_pipeline.sh samples.list &`
. Dependencies :
-
`config.sh`
...
...
getResults.py
View file @
b2154f22
...
...
@@ -133,8 +133,10 @@ if __name__ == '__main__':
sys
.
exit
(
1
)
with
open
(
sys
.
argv
[
1
])
as
samples_list
:
samples
=
[]
for
sample
in
sorted
(
samples_list
.
readlines
()):
samples
.
append
(
sample
.
rstrip
())
for
line
in
sorted
(
samples_list
.
readlines
()):
sample
=
line
.
rstrip
()
if
sample
:
samples
.
append
(
sample
)
os
.
makedirs
(
output_directory
,
exist_ok
=
True
)
for
locus
,
region
in
enumerate_variants
(
variant_catalog
):
print
(
locus
,
region
)
...
...
str_outliers.py
View file @
b2154f22
...
...
@@ -167,7 +167,9 @@ if __name__ == '__main__':
sys
.
exit
(
1
)
with
open
(
sys
.
argv
[
2
])
as
samples_list
:
samples
=
set
()
for
sample
in
samples_list
.
readlines
():
samples
.
add
(
sample
.
rstrip
())
for
line
in
samples_list
.
readlines
():
sample
=
line
.
rstrip
()
if
sample
:
samples
.
add
(
sample
)
limits
=
load_limits
()
display_outliers
(
sys
.
argv
[
1
],
limits
,
samples
)
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