Skip to content
Projects
Groups
Snippets
Help
This project
Loading...
Sign in / Register
Toggle navigation
S
STR
Project
Project
Details
Activity
Cycle Analytics
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Charts
Issues
0
Issues
0
List
Board
Labels
Milestones
Merge Requests
0
Merge Requests
0
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Charts
Wiki
Wiki
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Charts
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
Anne-Sophie Denommé-Pichon
STR
Commits
4b011eed
Commit
4b011eed
authored
Jul 31, 2020
by
Anne-Sophie Denommé-Pichon
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Add sample list file as argument
parent
1e638b24
Show whitespace changes
Inline
Side-by-side
Showing
9 changed files
with
60 additions
and
29 deletions
+60
-29
README.md
README.md
+3
-2
launch_pipeline.sh
launch_pipeline.sh
+1
-1
launch_pipeline_ehdn_outlier.sh
launch_pipeline_ehdn_outlier.sh
+15
-6
launch_results.sh
launch_results.sh
+1
-1
launch_str_outliers.sh
launch_str_outliers.sh
+1
-1
pipeline.sh
pipeline.sh
+1
-1
pipeline_ehdn_outlier.sh
pipeline_ehdn_outlier.sh
+10
-1
str_outliers.py
str_outliers.py
+1
-1
wrapper_ehdn_outlier.sh
wrapper_ehdn_outlier.sh
+27
-15
No files found.
README.md
View file @
4b011eed
...
...
@@ -20,13 +20,14 @@ For now, scripts have to be launched from the clone directory.
-
`wrapper_gangstr.sh`
-
`wrapper_transfer.sh`
-
`wrapper_tredparse.sh`
4.
Optional: launch
`launch_pipeline_ehdn_outlier.sh`
:
`nohup ./launch_pipeline_ehdn_outlier.sh &`
. Dependencies:
4.
Optional: launch
`launch_pipeline_ehdn_outlier.sh`
:
`nohup ./launch_pipeline_ehdn_outlier.sh
samples.list
&`
. Dependencies:
-
`config.sh`
-
`samples.list`
-
`pipeline_ehdn_outlier.sh`
-
`wrapper_ehdn_outlier.sh`
5.
Launch
`launch_results.sh`
:
`nohup ./launch_results.sh samples.list &`
. Dependencies:
-
`config.sh`
-
`sample.list`
-
`sample
s
.list`
-
`patho.csv`
-
`getResults.py`
-
`launch_str_outliers.sh`
...
...
launch_pipeline.sh
View file @
4b011eed
...
...
@@ -6,7 +6,7 @@
## Author: Anne-Sophie Denommé-Pichon
## Description: script to launch the pipeline for STR detection. Receive multiple samples: one sample per line
# $1 : first argument in the command line : a list containing one sample per line, for ex
e
mple samples.list
# $1 : first argument in the command line : a list containing one sample per line, for ex
a
mple samples.list
SAMPLES
=
"
$1
"
# Check if sample is specified
...
...
launch_pipeline_ehdn_outlier.sh
View file @
4b011eed
...
...
@@ -6,14 +6,23 @@
## Author : Anne-Sophie Denommé-Pichon
## Description : script to launch the pipeline for STR detection with EHDN outlier
# $1 : first argument in the command line : a list containing one sample per line, for example samples.list
SAMPLES
=
"
$1
"
# Check if samples list file is specified
if
[
-z
"
$SAMPLES
"
]
then
echo
"List of samples is not specified"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
exit
1
fi
# Source configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
(
cd
"
$OUTPUTDIR
"
printf
"%s
\n
"
*
)
|
"
$PARALLEL
"
\
# Parallel allow to parallelize the processing of multiple samples ({}: one line in samples.list ; $SAMPLES: the file name: samples.list)
"
$PARALLEL
"
\
--jobs
"
$PARALLEL_JOB_COUNT
"
\
--line-buffer
\
"
$(
dirname
"
$0
"
)
/pipeline_ehdn_outlier.sh"
"
$(
dirname
"
$0
"
)
/pipeline_ehdn_outlier.sh"
{}
"
$SAMPLES
"
\
<
"
$SAMPLES
"
launch_results.sh
View file @
4b011eed
...
...
@@ -6,7 +6,7 @@
## Author: Anne-Sophie Denommé-Pichon
## Description: script to launch the pipeline for getting STR detection results. Receive multiple samples: one sample per line
# $1 : first argument in the command line : a list containing one sample per line, for ex
e
mple samples.list
# $1 : first argument in the command line : a list containing one sample per line, for ex
a
mple samples.list
SAMPLES
=
"
$1
"
# Check if sample is specified
...
...
launch_str_outliers.sh
View file @
4b011eed
...
...
@@ -9,7 +9,7 @@
# Source configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# $1 : first argument in the command line : a list containing one sample per line, for ex
e
mple samples.list
# $1 : first argument in the command line : a list containing one sample per line, for ex
a
mple samples.list
SAMPLES
=
"
$1
"
# Check if sample is specified
...
...
pipeline.sh
View file @
4b011eed
...
...
@@ -61,7 +61,7 @@ qsub -wd "$WD" -pe smp 4 -o "$LOGDIR" -e "$LOGDIR" -q "$COMPUTE_QUEUE" -N "gangs
# Launch ehdn profile
mkdir
-p
"
$STRDIR
/ehdn"
qsub
-wd
"
$WD
"
-pe
smp 4
-o
"
$LOGDIR
"
-e
"
$LOGDIR
"
-q
"
$COMPUTE_QUEUE
"
-N
"ehdn_
$SAMPLE
"
-hold_jid
"
$TRANSFER_JOB
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$STRDIR
/ehdn/
$SAMPLE
"
,LOGFILE
=
"
$LOGDIR
/ehdn_
$SAMPLE
.
$DATE
.log"
"
$WD
/wrapper_ehdn_profile.sh"
qsub
-wd
"
$WD
"
-pe
smp 4
-o
"
$LOGDIR
"
-e
"
$LOGDIR
"
-q
"
$COMPUTE_QUEUE
"
-N
"ehdn_
$SAMPLE
"
-hold_jid
"
$TRANSFER_JOB
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$STRDIR
/ehdn/
$SAMPLE
"
,LOGFILE
=
"
$LOGDIR
/ehdn_
profile_
$SAMPLE
.
$DATE
.log"
"
$WD
/wrapper_ehdn_profile.sh"
# Delete transfered bam and bai
#if [ "x$TRANSFER" = "xyes" ]
...
...
pipeline_ehdn_outlier.sh
View file @
4b011eed
...
...
@@ -10,6 +10,15 @@
.
"
$(
dirname
"
$0
"
)
/config.sh"
CASE
=
"
$1
"
SAMPLES
=
"
$2
"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
WD
=
"
$(
dirname
"
$(
readlink
-f
"
$0
"
)
"
)
"
qsub
-wd
"
$(
dirname
"
$(
readlink
-f
"
$0
"
)
"
)
"
-pe
smp 1
-q
"
$COMPUTE_QUEUE
"
-N
"ehdn_outlier_
$CASE
"
-sync
y
-v
CASE
=
"
$CASE
"
wrapper_ehdn_outlier.sh
LOGDIR
=
"
$OUTPUTDIR
/logs"
STRDIR
=
"
$OUTPUTDIR
/str"
mkdir
-p
"
$LOGDIR
"
"
$STRDIR
"
qsub
-wd
"
$WD
"
-pe
smp 1
-o
"
$LOGDIR
"
-e
"
$LOGDIR
"
-q
"
$COMPUTE_QUEUE
"
-N
"ehdn_outlier_
$CASE
"
-sync
y
-v
CASE
=
"
$CASE
"
,SAMPLES
=
"
$SAMPLES
"
,LOGFILE
=
"
$LOGDIR
/ehdn_outlier_
$CASE
.
$DATE
.log"
"
$WD
/wrapper_ehdn_outlier.sh"
str_outliers.py
View file @
4b011eed
...
...
@@ -102,7 +102,7 @@ def display_outliers(locus, limits, samples):
print
(
'Input file is empty'
,
file
=
sys
.
stderr
)
sys
.
exit
(
1
)
# outlier threshold (ex
e
mple: 5%)
# outlier threshold (ex
a
mple: 5%)
for
tool
,
tool_values
in
tools_values
.
items
():
# Test if there is at least one value given by the tool
if
tool_values
:
...
...
wrapper_ehdn_outlier.sh
View file @
4b011eed
...
...
@@ -9,8 +9,13 @@
# Source the configuration file
.
./config.sh
# Log file path option
if
[
-z
"
$LOGFILE
"
]
then
LOGFILE
=
ehdn_outlier.
$(
date
+
"%F_%H-%M-%S"
)
.log
fi
# Logging
LOGFILE
=
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.ehdn_outlier.
$(
date
+
"%F_%H-%M-%S"
)
.log"
exec
1>>
"
$LOGFILE
"
2>&1
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: START"
...
...
@@ -22,21 +27,28 @@ then
exit
1
fi
# Check if samples list file is specified
if
[
-z
"
$SAMPLES
"
]
then
echo
"Sample list file is not specified"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
exit
1
fi
# Generate manifest for one patient with all samples (to write lines in the file)
cd
"
$OUTPUTDIR
"
for
sample
in
*
while
read
sample
do
# Check if str_profile.json exists
if
[
-f
"
$OUTPUTDIR
/
$sample
/ehdn/
$sample
.str_profile.json"
]
if
[
-f
"
$OUTPUTDIR
/
$sample
/
str/
ehdn/
$sample
.str_profile.json"
]
then
if
[
"x
$sample
"
=
"x
$CASE
"
]
then
echo
-e
"
$sample
\t
case
\t
$OUTPUTDIR
/
$sample
/ehdn/
$sample
.str_profile.json"
echo
-e
"
$sample
\t
case
\t
$OUTPUTDIR
/
$sample
/str
/ehdn/
$sample
.str_profile.json"
else
echo
-e
"
$sample
\t
control
\t
$OUTPUTDIR
/
$sample
/ehdn/
$sample
.str_profile.json"
echo
-e
"
$sample
\t
control
\t
$OUTPUTDIR
/
$sample
/str
/ehdn/
$sample
.str_profile.json"
fi
fi
done
>
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
done
<
"
$SAMPLES
"
>
"
$OUTPUTDIR
/
$CASE
/str
/ehdn/
$CASE
.manifest.tsv"
ehdn_outlier_exitcode
=
$?
...
...
@@ -50,8 +62,8 @@ fi
# Generate multisampleprofile for one patient with all samples
"
$EHDN
"
merge
\
--reference
"
$REFERENCE
"
\
--manifest
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--output-prefix
"
$CASE
/ehdn/
$CASE
"
--manifest
"
$OUTPUTDIR
/
$CASE
/
str/
ehdn/
$CASE
.manifest.tsv"
\
--output-prefix
"
$CASE
/
str/
ehdn/
$CASE
"
ehdn_outlier_exitcode
=
$?
...
...
@@ -64,9 +76,9 @@ fi
# Run locus-based comparison analysis
"
$EHDN_OUTLIER
"
locus
\
--manifest
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.outlier_locus.tsv"
--manifest
"
$OUTPUTDIR
/
$CASE
/
str/
ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$OUTPUTDIR
/
$CASE
/
str/
ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$OUTPUTDIR
/
$CASE
/
str/
ehdn/
$CASE
.outlier_locus.tsv"
ehdn_outlier_exitcode
=
$?
...
...
@@ -80,9 +92,9 @@ fi
# Run motif_based comparison analysis
"
$EHDN_OUTLIER
"
motif
\
--manifest
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$OUTPUTDIR
/
$CASE
/ehdn/
$CASE
.outlier_motif.tsv"
--manifest
"
$OUTPUTDIR
/
$CASE
/
str/
ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$OUTPUTDIR
/
$CASE
/
str/
ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$OUTPUTDIR
/
$CASE
/
str/
ehdn/
$CASE
.outlier_motif.tsv"
ehdn_outlier_exitcode
=
$?
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment