From 175f36403df8f498254a3dff8d9f702ecc203248 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Thu, 24 Sep 2020 10:09:03 +1000
Subject: [PATCH] generate commands to run array scripts for lastz and
repeatMasker
---
cross_species_comparison/scripts/lastz.sh | 17 +++++++++++++++++
.../scripts/repeatMasker.sh | 18 ++++++++++++++++++
2 files changed, 35 insertions(+)
create mode 100644 cross_species_comparison/scripts/lastz.sh
create mode 100644 cross_species_comparison/scripts/repeatMasker.sh
diff --git a/cross_species_comparison/scripts/lastz.sh b/cross_species_comparison/scripts/lastz.sh
new file mode 100644
index 0000000..6eed081
--- /dev/null
+++ b/cross_species_comparison/scripts/lastz.sh
@@ -0,0 +1,17 @@
+##!/usr/bin/env bash
+
+## This script loops through all scaffolds in the dunnart genome and
+## generates a separate lastz command for each scaffold
+## These commands are then used in a slurm array script to run jobs in parallel
+
+TRA=($(for file in *.fa; do echo $file |cut -d "." -f 1;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+echo 'lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/pun$
+
+done
diff --git a/cross_species_comparison/scripts/repeatMasker.sh b/cross_species_comparison/scripts/repeatMasker.sh
new file mode 100644
index 0000000..fc918a4
--- /dev/null
+++ b/cross_species_comparison/scripts/repeatMasker.sh
@@ -0,0 +1,18 @@
+##!/usr/bin/env bash
+
+## This script loops through all scaffolds in the dunnart genome and
+## generates a separate RepeatMasker command for each scaffold
+## These commands are then used in a slurm array script to run jobs in parallel
+
+TRA=($(for file in *.fa; do echo $file |cut -d "." -f 1;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+echo 'RepeatMasker -q -xsmall smiCra1/'${tr}'.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/'
+
+
+done
--
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