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DIADE
dynadiv
GrAnnoT
Commits
cca80b85
Commit
cca80b85
authored
9 months ago
by
francois.sabot_ird.fr
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adding loops
parent
264e1641
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GrAnnoT/codes4publications/liftOffChainer.sh
+34
-5
34 additions, 5 deletions
GrAnnoT/codes4publications/liftOffChainer.sh
with
34 additions
and
5 deletions
GrAnnoT/codes4publications/liftOffChainer.sh
+
34
−
5
View file @
cca80b85
...
...
@@ -29,15 +29,16 @@
#SBATCH --export=ALL
#SBATCH --mail-user francois.sabot@ird.fr
#SBATCH --mail-type=ALL
#SBATCH -p gpu
#SBATCH -p temp
#SBATCH -A temp
#SBATCH -c 24
#SBATCH -J LOchain
#SBATCH -nodelist=node7
#Data recovery
ANNOTATION
=
$1
SEQFOLDER
=
$2
OUTPUT
=
$3
ANNOTATION
=
$1
SEQFOLDER
=
$2
REFERENCESEQ
=
$3
OUTPUT
=
$4
#Modules used
module load liftoff/1.6.3
...
...
@@ -46,3 +47,31 @@ module load liftoff/1.6.3
# [-chroms TXT] [-unplaced TXT] [-copies] [-sc SC] [-overlap O] [-mismatch M] [-gap_open GO] [-gap_extend GE] [-polish] [-cds]
# target reference""
#Liftoff in GFF mode
echo
-e
"########################################
\n\n
Running in GFF mode
\n\n
"
for
TARGETSEQ
in
`
ls
$SEQFOLDER
`
;
do
if
[[
$TARGETSEQ
==
$REFERENCESEQ
]]
;
then
continue
fi
OUTFILE
=
$OUTPUT
.
"/"
.
$SEQFILE
.
".gff"
UNMAPPED
==
$OUTPUT
.
"/"
.
$SEQFILE
.
"_unmapped.txt"
echo
-e
"
\n
Running for
$TARGETSEQ
\n
"
>>
timelog.txt
LIFTCOM
=
'time liftoff -g $ANNOTATION -o $OUTFILE -u $UNMAPPED -p 1 $TARGETSEQ $REFERENCESEQ'
$LIFTCOM
>>
timelog.txt
||
exit
135
done
#Liftoff in DDB mode
echo
-e
"########################################
\n\n
Running in DB mode
\n\n
"
for
TARGETSEQ
in
`
ls
$SEQFOLDER
`
;
do
if
[[
$TARGETSEQ
==
$REFERENCESEQ
]]
;
then
continue
fi
DB
=
${
ANNOTATION
}
"_db"
OUTFILE
=
$OUTPUT
.
"/"
.
$SEQFILE
.
".db.gff"
UNMAPPED
==
$OUTPUT
.
"/"
.
$SEQFILE
.
"_unmappeddb.txt"
echo
-e
"
\n
Running for
$TARGETSEQ
\n
"
>>
timelog.txt
LIFTCOMDB
=
'time liftoff -db $DB -o $OUTFILE -u $UNMAPPED -p 1 $TARGETSEQ $REFERENCESEQ'
$LIFTCOMDB
>>
timelog.txt
||
exit
135
done
#{ date ; time liftoff -o prout -g locus.gff IR64_GuppyFlyeMedakaRagtag.fasta irgsp5_complete.fasta ; } > time.log 2>&1 && tail -n 10 time.log > time2.log
\ No newline at end of file
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