From 5e7f70fb56ce0e6298ef8bebb55c5812d26095bd Mon Sep 17 00:00:00 2001
From: mcariou <115-mcariou@users.noreply.gitbio.ens-lyon.fr>
Date: Mon, 22 Nov 2021 17:43:23 +0100
Subject: [PATCH] correct lp2300 script
---
script/.4_parse_PSIblastTMP.sh.swp | Bin 12288 -> 0 bytes
script/runscript.sh | 8 ++++++--
script/runscript_78Lp_step34.sh | 22 ++++++++++++++++++++++
script/runscript_lp2300_step3.sh | 20 ++++++++++++++++++++
script/runscript_lp2300_step4.sh | 26 ++++++++++++++++++++++++++
5 files changed, 74 insertions(+), 2 deletions(-)
delete mode 100644 script/.4_parse_PSIblastTMP.sh.swp
create mode 100755 script/runscript_78Lp_step34.sh
create mode 100755 script/runscript_lp2300_step3.sh
create mode 100755 script/runscript_lp2300_step4.sh
diff --git a/script/.4_parse_PSIblastTMP.sh.swp b/script/.4_parse_PSIblastTMP.sh.swp
deleted file mode 100644
index ec2f9478529362620ec5b338ea323d8923ffbeea..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
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diff --git a/script/runscript.sh b/script/runscript.sh
index 8f721b0..a22df09 100755
--- a/script/runscript.sh
+++ b/script/runscript.sh
@@ -12,10 +12,14 @@
#$ -e /home/mcariou/2021_legio/log/
module load R
-
-./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.1 0.1 1
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.5 1
+
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.3 1
+
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.3 1
diff --git a/script/runscript_78Lp_step34.sh b/script/runscript_78Lp_step34.sh
new file mode 100755
index 0000000..15f215c
--- /dev/null
+++ b/script/runscript_78Lp_step34.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+#$ -S /bin/bash
+## name of the job to follow them
+#$ -N runscript34
+## 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/
+
+
+/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
+
+
+## Doesn't accomodate multi query yet
+#/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/78Lp_uniprot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
+
+
+# fin
diff --git a/script/runscript_lp2300_step3.sh b/script/runscript_lp2300_step3.sh
new file mode 100755
index 0000000..a0d5d5a
--- /dev/null
+++ b/script/runscript_lp2300_step3.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+#$ -S /bin/bash
+## name of the job to follow them
+#$ -N runscript3
+## 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/
+
+
+/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/lpg2300_prot.fasta ~/2021_legio/out_blastn/
+
+
+
+
+# fin
diff --git a/script/runscript_lp2300_step4.sh b/script/runscript_lp2300_step4.sh
new file mode 100755
index 0000000..a22df09
--- /dev/null
+++ b/script/runscript_lp2300_step4.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+#$ -S /bin/bash
+## name of the job to follow them
+#$ -N runscript4
+## 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 R
+
+
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
+
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.5 1
+
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.3 1
+
+./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.3 1
+
+
+
+# fin
--
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