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Anne-Sophie Denommé-Pichon
STR
Commits
c1243e16
Commit
c1243e16
authored
Jul 31, 2020
by
Anne-Sophie Denommé-Pichon
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Update paths for results scripts
parent
4b011eed
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3 changed files
with
5 additions
and
8 deletions
+5
-8
getResults.py
getResults.py
+3
-3
launch_str_outliers.sh
launch_str_outliers.sh
+1
-1
str_outliers.py
str_outliers.py
+1
-4
No files found.
getResults.py
View file @
c1243e16
...
...
@@ -122,9 +122,9 @@ def get_results(locus, region, samples):
if
sample
not
in
previous_results
:
file_path
=
os
.
path
.
join
(
input_directory
,
sample
)
print
(
file_path
)
eh
=
get_eh_results
(
os
.
path
.
join
(
file_path
,
f
'eh/{sample}.vcf'
),
region
)
tred
=
get_tred_results
(
os
.
path
.
join
(
file_path
,
f
'tredparse/{sample}.tred.vcf.gz'
),
region
)
gang
=
get_gang_results
(
os
.
path
.
join
(
file_path
,
f
'gangstr/{sample}.vcf'
),
region
)
eh
=
get_eh_results
(
os
.
path
.
join
(
file_path
,
f
'
str/
eh/{sample}.vcf'
),
region
)
tred
=
get_tred_results
(
os
.
path
.
join
(
file_path
,
f
'
str/
tredparse/{sample}.tred.vcf.gz'
),
region
)
gang
=
get_gang_results
(
os
.
path
.
join
(
file_path
,
f
'
str/
gangstr/{sample}.vcf'
),
region
)
result_file
.
write
(
f
'{sample}
\t
{eh}
\t
{tred}
\t
{gang}
\n
'
)
if
__name__
==
'__main__'
:
...
...
launch_str_outliers.sh
View file @
c1243e16
...
...
@@ -21,7 +21,7 @@ then
fi
SCRIPT
=
"
$(
dirname
"
$(
readlink
-f
"
$0
"
)
"
)
/str_outliers.py"
SAMPLES
=
"
$(
dirname
"
$(
readlink
-f
"
$0
"
)
"
)
/
$SAMPLES
"
SAMPLES
=
"
$(
readlink
-f
"
$SAMPLES
"
)
"
cd
"
$RESULTS_OUTPUTDIR
"
||
exit
1
...
...
str_outliers.py
View file @
c1243e16
...
...
@@ -6,7 +6,6 @@
## Author : Anne-Sophie Denommé-Pichon
## Description : script to get automatically outliers from expansion pipeline results from getResults.py
import
collections
import
csv
import
logging
...
...
@@ -16,8 +15,6 @@ import os.path
import
scipy.stats
import
sys
output_directory
=
None
zscore_threshold
=
None
percentile_threshold
=
None
...
...
@@ -163,7 +160,7 @@ def display_outliers(locus, limits, samples):
if
__name__
==
'__main__'
:
if
len
(
sys
.
argv
)
!=
3
:
print
(
f
'Usage: {sys.argv[0].split(os.sep)[-1]} <LOCUS> <SAMPLE.LIST>'
,
file
=
sys
.
stderr
)
print
(
f
'Usage: {sys.argv[0].split(os.sep)[-1]} <LOCUS> <SAMPLE
S
.LIST>'
,
file
=
sys
.
stderr
)
sys
.
exit
(
1
)
with
open
(
sys
.
argv
[
2
])
as
samples_list
:
samples
=
set
()
...
...
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