From e141e9e72edeb7468bc022720771026f404ec54d Mon Sep 17 00:00:00 2001
From: Xavier <53685506+Nevermore233@users.noreply.github.com>
Date: Mon, 4 Mar 2024 19:57:00 +0800
Subject: [PATCH] Add files via upload

---
 data/sh_script/add_ART-Random.sh              | 10 ++++++++
 data/sh_script/add_MS+Seq-Gen+ART_sample1.sh  | 10 ++++++++
 data/sh_script/remove_ART-Random.sh           | 11 +++++++++
 .../remove_MS+Seq-Gen+ART_sample1.sh          | 11 +++++++++
 data/sh_script/sim_ART-Random.sh              | 17 ++++++++++++++
 data/sh_script/sim_MS+Seq-Gen+ART_sample1.sh  | 17 ++++++++++++++
 .../trisomy_sim_MS+Seq-Gen+ART_sample1.sh     | 23 +++++++++++++++++++
 data/sh_script/trisomy_sim__ART-Random.sh     | 23 +++++++++++++++++++
 8 files changed, 122 insertions(+)
 create mode 100644 data/sh_script/add_ART-Random.sh
 create mode 100644 data/sh_script/add_MS+Seq-Gen+ART_sample1.sh
 create mode 100644 data/sh_script/remove_ART-Random.sh
 create mode 100644 data/sh_script/remove_MS+Seq-Gen+ART_sample1.sh
 create mode 100644 data/sh_script/sim_ART-Random.sh
 create mode 100644 data/sh_script/sim_MS+Seq-Gen+ART_sample1.sh
 create mode 100644 data/sh_script/trisomy_sim_MS+Seq-Gen+ART_sample1.sh
 create mode 100644 data/sh_script/trisomy_sim__ART-Random.sh

diff --git a/data/sh_script/add_ART-Random.sh b/data/sh_script/add_ART-Random.sh
new file mode 100644
index 0000000..c50fe2a
--- /dev/null
+++ b/data/sh_script/add_ART-Random.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+for ((i=0; i<=999; i++))
+do
+    modified_file="./sam/trisomy/${i}_sample_modified.sam"
+    original_file="./sam/sample_${i}.sam"
+
+    cat "$modified_file" >> "$original_file"
+    echo "Appended $modified_file to $original_file"
+done
\ No newline at end of file
diff --git a/data/sh_script/add_MS+Seq-Gen+ART_sample1.sh b/data/sh_script/add_MS+Seq-Gen+ART_sample1.sh
new file mode 100644
index 0000000..48d3a24
--- /dev/null
+++ b/data/sh_script/add_MS+Seq-Gen+ART_sample1.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+for ((i=0; i<=999; i++))
+do
+    modified_file="./sam-ms/trisomy-ms/${i}_sample_modified.sam"
+    original_file="./sam-ms/sample_${i}.sam"
+
+    cat "$modified_file" >> "$original_file"
+    echo "Appended $modified_file to $original_file"
+done
\ No newline at end of file
diff --git a/data/sh_script/remove_ART-Random.sh b/data/sh_script/remove_ART-Random.sh
new file mode 100644
index 0000000..6f7d13b
--- /dev/null
+++ b/data/sh_script/remove_ART-Random.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+for ((i=0; i<=999; i++))
+do
+    input_file="./sam/trisomy/${i}_sample.sam"
+    output_file="./sam/trisomy/${i}_sample_modified.sam"
+    
+    sed '1,3d' "$input_file" > "$output_file"
+    
+    echo "Processed $input_file, saved as $output_file"
+done
\ No newline at end of file
diff --git a/data/sh_script/remove_MS+Seq-Gen+ART_sample1.sh b/data/sh_script/remove_MS+Seq-Gen+ART_sample1.sh
new file mode 100644
index 0000000..b0ddb35
--- /dev/null
+++ b/data/sh_script/remove_MS+Seq-Gen+ART_sample1.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+for ((i=0; i<=999; i++))
+do
+    input_file="./sam-ms/trisomy-ms/${i}_sample.sam"
+    output_file="./sam-ms/trisomy-ms/${i}_sample_modified.sam"
+    
+    sed '1,3d' "$input_file" > "$output_file"
+    
+    echo "Processed $input_file, saved as $output_file"
+done
\ No newline at end of file
diff --git a/data/sh_script/sim_ART-Random.sh b/data/sh_script/sim_ART-Random.sh
new file mode 100644
index 0000000..1385693
--- /dev/null
+++ b/data/sh_script/sim_ART-Random.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+#illumina test examples
+art=../art_illumina
+f_value="f_value_ART-Random.txt"
+> $f_value
+
+for ((i=0; i<=1999; i++))
+do
+    output_file="sample_${i}"
+    
+    # Generate a random floating point number within the range of [0.1, 0.5]
+    random_float=$(awk -v min=0.1 -v max=0.5 'BEGIN{srand(); print min+rand()*(max-min)}')
+    
+    echo $random_float >> $f_value
+     
+    $art -ss HS25 -sam -i ./ref_ART-Random.fa -l 35 -p -f $random_float -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam/${output_file}"
+done
\ No newline at end of file
diff --git a/data/sh_script/sim_MS+Seq-Gen+ART_sample1.sh b/data/sh_script/sim_MS+Seq-Gen+ART_sample1.sh
new file mode 100644
index 0000000..921b4b0
--- /dev/null
+++ b/data/sh_script/sim_MS+Seq-Gen+ART_sample1.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+#illumina test examples
+art=../art_illumina
+f_value="f_value_MS+Seq-Gen+ART_sample1.txt"
+> $f_value
+
+for ((i=0; i<=1999; i++))
+do
+    output_file="sample_${i}"
+    
+    # Generate a random floating point number within the range of [0.1, 0.5]
+    random_float=$(awk -v min=0.1 -v max=0.5 'BEGIN{srand(); print min+rand()*(max-min)}')
+    
+    echo $random_float >> $f_value
+     
+    $art -ss HS25 -sam -i ./ref_MS+Seq-Gen+ART_sample1.fa -l 35 -p -f $random_float -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam-ms/${output_file}"
+done
\ No newline at end of file
diff --git a/data/sh_script/trisomy_sim_MS+Seq-Gen+ART_sample1.sh b/data/sh_script/trisomy_sim_MS+Seq-Gen+ART_sample1.sh
new file mode 100644
index 0000000..cc8c817
--- /dev/null
+++ b/data/sh_script/trisomy_sim_MS+Seq-Gen+ART_sample1.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#illumina test examples
+art=../art_illumina
+for ((i=0; i<=333; i++))
+do
+    output_file="${i}_sample"
+ 
+    $art -ss HS25 -sam -i ./ref_MS+Seq-Gen+ART_sample1_chr13.fa -l 35 -p -f 0.2  -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam-ms/trisomy-ms/${output_file}"
+done
+
+for ((i=334; i<=666; i++))
+do
+    output_file="${i}_sample"
+ 
+    $art -ss HS25 -sam -i ./ref_MS+Seq-Gen+ART_sample1_chr18.fa -l 35 -p -f 0.2  -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam-ms/trisomy-ms/${output_file}"
+done
+
+for ((i=667; i<=999; i++))
+do
+    output_file="${i}_sample"
+ 
+    $art -ss HS25 -sam -i ./ref_MS+Seq-Gen+ART_sample1_chr21.fa -l 35 -p -f 0.2  -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam-ms/trisomy-ms/${output_file}"
+done
\ No newline at end of file
diff --git a/data/sh_script/trisomy_sim__ART-Random.sh b/data/sh_script/trisomy_sim__ART-Random.sh
new file mode 100644
index 0000000..af64f70
--- /dev/null
+++ b/data/sh_script/trisomy_sim__ART-Random.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#illumina test examples
+art=../art_illumina
+for ((i=0; i<=333; i++))
+do
+    output_file="${i}_sample"
+ 
+    $art -ss HS25 -sam -i ./ref_ART-Random_chr13.fa -l 35 -p -f 0.2  -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam/trisomy/${output_file}"
+done
+
+for ((i=334; i<=666; i++))
+do
+    output_file="${i}_sample"
+ 
+    $art -ss HS25 -sam -i ./ref_ART-Random_chr18.fa -l 35 -p -f 0.2  -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam/trisomy/${output_file}"
+done
+
+for ((i=667; i<=999; i++))
+do
+    output_file="${i}_sample"
+ 
+    $art -ss HS25 -sam -i ./ref_ART-Random_chr21.fa -l 35 -p -f 0.2  -m 100 -s 5 -M -ir 0.005 -ir2 0.005 -dr 0.005 -dr2 0.005 -na -o "./sam/trisomy/${output_file}"
+done
\ No newline at end of file