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mcariou
phylolegio
Commits
5a8bf2b1
Commit
5a8bf2b1
authored
Jan 17, 2022
by
mcariou
Browse files
V2
parent
e971674a
Changes
2
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script/2_make_db.sh
View file @
5a8bf2b1
...
...
@@ -20,11 +20,11 @@ module purge
HOME
=
"/home/mcariou/2021_legio/"
OUT
=
$HOME
"blastdb/phyloref/"
OUT
=
$HOME
"blastdb/phyloref
_V2
/"
CAT
=
$OUT
"/cat_phyloref_cds.fasta"
CATPROT
=
$OUT
"/cat_phyloref_pep.fasta"
Trans
=
"/home/mcariou/2020_Attaiech/prot_db/Transdecoder/"
TAB
=
$HOME
"/phylolegio/doc/tabAss.txt"
TAB
=
$HOME
"/phylolegio/doc/tabAss
_V2
.txt"
mkdir
-p
$OUT
...
...
@@ -34,14 +34,14 @@ mkdir -p $OUT
if
[[
-s
$CAT
]]
;
then
echo
"cat already exists"
else
for
genome
in
`
cat
$TAB
|
sed
'1d'
|
awk
'{print $1}'
`
for
genome
in
`
cat
$TAB
|
sed
'1d'
|
awk
-F
";"
'{print $1}'
`
do
file
=
${
Trans
}
/
${
genome
}*
/longest_orfs.cds
file2
=
`
echo
$file
`
if
[[
-s
$file2
]]
;
then
cat
$file2
>>
$CAT
else
echo
"doesn't:
$file
2
"
echo
"doesn't:
$file
"
fi
done
fi
...
...
script/psmn/runscript_78Lp_V2.sh
0 → 100755
View file @
5a8bf2b1
#!/bin/bash
#$ -S /bin/bash
## name of the job to follow them
#$ -N runscript_V2
## name of the queue to be used
#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
#$ -cwd
#$ -V
## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
## the dirs must exist before job is launched
#$ -o /home/mcariou/2021_legio/log/
#$ -e /home/mcariou/2021_legio/log/
module load trimal
/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref_V2/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblast.sh ~/2021_legio/out_blastn/78Lp_uniprot_V2.psiblast ~/2021_legio/phylolegio/doc/tabAss_V2.txt ~/2021_legio/fasta/78Lp_V2 ~/2021_legio/genes/78Lp_uniprot.fasta 0.0001 0.5 0.5 1
/home/mcariou/2021_legio/phylolegio/script/5_cat_aln_phy.sh ~/2021_legio/fasta/78Lp_V2/
# fin
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