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Anne-Sophie Denommé-Pichon
STR
Commits
b069b9cc
Commit
b069b9cc
authored
Feb 15, 2020
by
Anne-Sophie Denommé-Pichon
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Change ehdn outlier analysis script to handle qsub
parent
62eed830
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3 changed files
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118 additions
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105 deletions
+118
-105
ehdn_getmultisampleprofile.sh
ehdn/ehdn_getmultisampleprofile.sh
+0
-43
ehdn_outlier.sh
ehdn/ehdn_outlier.sh
+0
-62
wrapper_ehdn_outlier.sh
wrapper_ehdn_outlier.sh
+118
-0
No files found.
ehdn/ehdn_getmultisampleprofile.sh
deleted
100755 → 0
View file @
62eed830
#! /bin/sh
### ASDP PIPELINE ###
## ehdn_getmanifest.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to generate automatically a manifest and multisampleprofile by patient in a tsv format
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20200215
## last revision date : 20200215
## Known bugs : None
EHDN
=
"/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
REFERENCE
=
"/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
WORKDIR
=
"/work/gad/shared/analyse/STR/pipeline"
cd
"
$WORKDIR
"
# Generate manifest and multisampleprofile by patient for all patients (to write file)
for case
in
dijen
*
do
# Generate manifest for one patient with all samples (to write lines in the file)
for
dijen
in
dijen
*
do
if
[
"x
$dijen
"
=
"x
$case
"
]
then
echo
-e
"
$dijen
\t
case
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
else
echo
-e
"
$dijen
\t
control
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
fi
done
>
"
$WORKDIR
/
$case
/ehdn/
$case
.manifest.tsv"
# Generate multisampleprofile for one patient with all samples
"
$EHDN
"
merge
\
--reference
"
$REFERENCE
"
\
--manifest
"
$WORKDIR
/
$case
/ehdn/
$case
.manifest.tsv"
\
--output-prefix
"
$case
/ehdn/
$case
"
done
ehdn/ehdn_outlier.sh
deleted
100755 → 0
View file @
62eed830
#! /bin/sh
### ASDP PIPELINE ###
## ehdn_getmanifest.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to generate automatically a manifest and multisampleprofile by patient in a tsv format
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20200215
## last revision date : 20200215
## Known bugs : None
EHDN
=
"/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
EHDN_OUTLIER
=
"/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py"
REFERENCE
=
"/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
WORKDIR
=
"/work/gad/shared/analyse/STR/pipeline"
cd
"
$WORKDIR
"
# Generate manifest and multisampleprofile by patient for all patients (to write file)
for case
in
dijen
*
do
# Generate manifest for one patient with all samples (to write lines in the file)
for
dijen
in
dijen
*
do
# Check if str_profile.json exists
if
[
-f
"
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
]
then
if
[
"x
$dijen
"
=
"x
$case
"
]
then
echo
-e
"
$dijen
\t
case
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
else
echo
-e
"
$dijen
\t
control
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
fi
fi
done
>
"
$WORKDIR
/
$case
/ehdn/
$case
.manifest.tsv"
# Generate multisampleprofile for one patient with all samples
"
$EHDN
"
merge
\
--reference
"
$REFERENCE
"
\
--manifest
"
$WORKDIR
/
$case
/ehdn/
$case
.manifest.tsv"
\
--output-prefix
"
$case
/ehdn/
$case
"
# Run locus-based comparison analysis
"
$EHDN_OUTLIER
"
locus
\
--manifest
"
$WORKDIR
/
$case
/ehdn/
$case
.manifest.tsv"
\
--multisample-profile
"
$WORKDIR
/
$case
/ehdn/
$case
.multisample_profile.json"
\
--output
"
$WORKDIR
/
$case
/ehdn/
$case
.outlier_locus.tsv"
# Run motif_based comparison analysis
"
$EHDN_OUTLIER
"
motif
\
--manifest
"
$WORKDIR
/
$case
/ehdn/
$case
.manifest.tsv"
\
--multisample-profile
"
$WORKDIR
/
$case
/ehdn/
$case
.multisample_profile.json"
\
--output
"
$WORKDIR
/
$case
/ehdn/
$case
.outlier_motif.tsv"
done
wrapper_ehdn_outlier.sh
0 → 100755
View file @
b069b9cc
#! /bin/sh
### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: FIXME
## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient
## Usage: FIXME
## Output: FIXME
## Requirements: FIXME
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date: 20200215
## Last revision date: 20200215
## Known bugs: None
EHDN
=
"/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
EHDN_OUTLIER
=
"/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py"
REFERENCE
=
"/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
WORKDIR
=
"/work/gad/shared/analyse/STR/pipeline"
# Log file path option
if
[
-z
"
$LOGFILE
"
]
then
LOGFILE
=
ehdn_outlier.
$(
date
+
"%F_%H-%M-%S"
)
.log
fi
# Logging
exec
1>>
"
$LOGFILE
"
2>&1
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: START"
# Check if case is specified
if
[
-z
"
$CASE
"
]
then
echo
"Dijen is not specified"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
ehdn_outlier.failed
exit
1
fi
# Generate manifest for one patient with all samples (to write lines in the file)
cd
"
$WORKDIR
"
for
dijen
in
dijen
*
do
# Check if str_profile.json exists
if
[
-f
"
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
]
then
if
[
"x
$dijen
"
=
"x
$CASE
"
]
then
echo
-e
"
$dijen
\t
case
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
else
echo
-e
"
$dijen
\t
control
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
fi
fi
done
>
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
ehdn_outlier_exitcode
=
$?
echo
"ehdn_outlier exit code :
$ehdn_outlier_exitcode
"
if
[
$ehdn_outlier_exitcode
!=
0
]
then
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
ehdn_outlier.failed
exit
1
fi
# Generate multisampleprofile for one patient with all samples
"
$EHDN
"
merge
\
--reference
"
$REFERENCE
"
\
--manifest
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--output-prefix
"
$CASE
/ehdn/
$CASE
"
ehdn_outlier_exitcode
=
$?
echo
"ehdn_outlier exit code :
$ehdn_outlier_exitcode
"
if
[
$ehdn_outlier_exitcode
!=
0
]
then
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
ehdn_outlier.failed
exit
1
fi
# Run locus-based comparison analysis
"
$EHDN_OUTLIER
"
locus
\
--manifest
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.outlier_locus.tsv"
ehdn_outlier_exitcode
=
$?
echo
"ehdn_outlier exit code :
$ehdn_outlier_exitcode
"
if
[
$ehdn_outlier_exitcode
!=
0
]
then
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
ehdn_outlier.failed
exit
1
fi
# Run motif_based comparison analysis
"
$EHDN_OUTLIER
"
motif
\
--manifest
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$WORKDIR
/
$CASE
/ehdn/
$CASE
.outlier_motif.tsv"
ehdn_outlier_exitcode
=
$?
echo
"ehdn_outlier exit code :
$ehdn_outlier_exitcode
"
if
[
$ehdn_outlier_exitcode
!=
0
]
then
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
ehdn_outlier.failed
exit
1
fi
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
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