BIO609

<br>

# .orange[BIO609 Introduction to `UNIX`/`Linux` and `Bash` Scripting]

#### 7<sup>th</sup> November, 2023

### Deepak Kumar Tanwar<br><br>.orange[URPP Evolution in Action <br>Embedded bioinformatician]

### <span><i class="fab  fa-twitter faa- animated " style=" color:#00acee;"></i></span> [.white[@d_k_tanwar]](https://twitter.com/d_k_tanwar)
### <span><i class="fas  fa-envelope faa- animated " style=" color:#2395fb;"></i></span> [.white[deepak.tanwar@evolution.uzh.ch]](mailto:deepak.tanwar@evolution.uzh.ch)
---

background-image: url("figs/01.png")
background-size: contain
background-position: 50% 5%

---

## .LARGE[.orange[UNIX]]

---

background-image: url("https://upload.wikimedia.org/wikipedia/commons/1/1b/Ken_Thompson_and_Dennis_Ritchie--1973.jpg")
background-size: 65%
background-position: 50% 10%

<div class="my-footer1" style="text-align: center;background-color:#FEE0D2;"> .blue[<b>Background</b>] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

.content-box-yellow[.Large[Ken Thompson]] &emsp;&emsp;&emsp;&emsp; .content-box-yellow[.Large[Dennis Ritchie]]

<div class="my-footer"><span> <a href="https://en.wikipedia.org/wiki/History_of_Unix"><svg viewBox="0 0 640 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M640 51.2l-.3 12.2c-28.1.8-45 15.8-55.8 40.3-25 57.8-103.3 240-155.3 358.6H415l-81.9-193.1c-32.5 63.6-68.3 130-99.2 193.1-.3.3-15 0-15-.3C172 352.3 122.8 243.4 75.8 133.4 64.4 106.7 26.4 63.4.2 63.7c0-3.1-.3-10-.3-14.2h161.9v13.9c-19.2 1.1-52.8 13.3-43.3 34.2 21.9 49.7 103.6 240.3 125.6 288.6 15-29.7 57.8-109.2 75.3-142.8-13.9-28.3-58.6-133.9-72.8-160-9.7-17.8-36.1-19.4-55.8-19.7V49.8l142.5.3v13.1c-19.4.6-38.1 7.8-29.4 26.1 18.9 40 30.6 68.1 48.1 104.7 5.6-10.8 34.7-69.4 48.1-100.8 8.9-20.6-3.9-28.6-38.6-29.4.3-3.6 0-10.3.3-13.6 44.4-.3 111.1-.3 123.1-.6v13.6c-22.5.8-45.8 12.8-58.1 31.7l-59.2 122.8c6.4 16.1 63.3 142.8 69.2 156.7L559.2 91.8c-8.6-23.1-36.4-28.1-47.2-28.3V49.6l127.8 1.1.2.5z"></path></svg> wikipedia.org/wiki/History_of_Unix</span></div>

???

- MIT, Bell Labs, and General Electric were developing **Multics**
- Can only be used by copy-writers
- Not free

---

background-image: url("https://www.helsinkitimes.fi/images/2021/Oct/linus.jpg")
background-size: 60%
background-position: 50% 10%

<div class="my-footer"><span> <a href="https://www.helsinkitimes.fi/finland/news-in-brief/20083-linus-torvalds-a-finnish-swede-who-changed-computing-forever.html"><svg viewBox="0 0 496 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M336.5 160C322 70.7 287.8 8 248 8s-74 62.7-88.5 152h177zM152 256c0 22.2 1.2 43.5 3.3 64h185.3c2.1-20.5 3.3-41.8 3.3-64s-1.2-43.5-3.3-64H155.3c-2.1 20.5-3.3 41.8-3.3 64zm324.7-96c-28.6-67.9-86.5-120.4-158-141.6 24.4 33.8 41.2 84.7 50 141.6h108zM177.2 18.4C105.8 39.6 47.8 92.1 19.3 160h108c8.7-56.9 25.5-107.8 49.9-141.6zM487.4 192H372.7c2.1 21 3.3 42.5 3.3 64s-1.2 43-3.3 64h114.6c5.5-20.5 8.6-41.8 8.6-64s-3.1-43.5-8.5-64zM120 256c0-21.5 1.2-43 3.3-64H8.6C3.2 212.5 0 233.8 0 256s3.2 43.5 8.6 64h114.6c-2-21-3.2-42.5-3.2-64zm39.5 96c14.5 89.3 48.7 152 88.5 152s74-62.7 88.5-152h-177zm159.3 141.6c71.4-21.2 129.4-73.7 158-141.6h-108c-8.8 56.9-25.6 107.8-50 141.6zM19.3 352c28.6 67.9 86.5 120.4 158 141.6-24.4-33.8-41.2-84.7-50-141.6h-108z"></path></svg> helsinkitimes.fi</span></div>

---

background-image: url("https://computerscience.chemeketa.edu/cs160Reader/_images/operating-system-logos.jpg")
background-size: 65%
background-position: 50% 50%

<div class="my-footer"><span> <a href="https://computerscience.chemeketa.edu/cs160Reader/OperatingSystems/OperatingSystems.html"><svg viewBox="0 0 496 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M336.5 160C322 70.7 287.8 8 248 8s-74 62.7-88.5 152h177zM152 256c0 22.2 1.2 43.5 3.3 64h185.3c2.1-20.5 3.3-41.8 3.3-64s-1.2-43.5-3.3-64H155.3c-2.1 20.5-3.3 41.8-3.3 64zm324.7-96c-28.6-67.9-86.5-120.4-158-141.6 24.4 33.8 41.2 84.7 50 141.6h108zM177.2 18.4C105.8 39.6 47.8 92.1 19.3 160h108c8.7-56.9 25.5-107.8 49.9-141.6zM487.4 192H372.7c2.1 21 3.3 42.5 3.3 64s-1.2 43-3.3 64h114.6c5.5-20.5 8.6-41.8 8.6-64s-3.1-43.5-8.5-64zM120 256c0-21.5 1.2-43 3.3-64H8.6C3.2 212.5 0 233.8 0 256s3.2 43.5 8.6 64h114.6c-2-21-3.2-42.5-3.2-64zm39.5 96c14.5 89.3 48.7 152 88.5 152s74-62.7 88.5-152h-177zm159.3 141.6c71.4-21.2 129.4-73.7 158-141.6h-108c-8.8 56.9-25.6 107.8-50 141.6zM19.3 352c28.6 67.9 86.5 120.4 158 141.6-24.4-33.8-41.2-84.7-50-141.6h-108z"></path></svg> computerscience.chemeketa.edu</span></div>

???

- Macintosh
- Linux
- Windows
- iOS
- Android
- FreeBSD

---

background-image: url("https://tecadmin.net/tutorial/wp-content/uploads/2017/10/linux-architecture-image.png")
background-size: 60%
background-position: 50% 50%

---

background-image: url("https://miro.medium.com/max/4800/0*EjMD-aiWVAoq09IB.jpg")
background-size: 65%
background-position: 50% 10%

background-image: url("https://developer.ibm.com/developer/default/tutorials/l-linux-shells/images/figure1.gif")
background-size: 80%
background-position: 50% 70%

## .Large[Evolution of shells in Linux]

<div class="my-footer"><span> <a href="https://developer.ibm.com/tutorials/l-linux-shells/"><svg viewBox="0 0 496 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M336.5 160C322 70.7 287.8 8 248 8s-74 62.7-88.5 152h177zM152 256c0 22.2 1.2 43.5 3.3 64h185.3c2.1-20.5 3.3-41.8 3.3-64s-1.2-43.5-3.3-64H155.3c-2.1 20.5-3.3 41.8-3.3 64zm324.7-96c-28.6-67.9-86.5-120.4-158-141.6 24.4 33.8 41.2 84.7 50 141.6h108zM177.2 18.4C105.8 39.6 47.8 92.1 19.3 160h108c8.7-56.9 25.5-107.8 49.9-141.6zM487.4 192H372.7c2.1 21 3.3 42.5 3.3 64s-1.2 43-3.3 64h114.6c5.5-20.5 8.6-41.8 8.6-64s-3.1-43.5-8.5-64zM120 256c0-21.5 1.2-43 3.3-64H8.6C3.2 212.5 0 233.8 0 256s3.2 43.5 8.6 64h114.6c-2-21-3.2-42.5-3.2-64zm39.5 96c14.5 89.3 48.7 152 88.5 152s74-62.7 88.5-152h-177zm159.3 141.6c71.4-21.2 129.4-73.7 158-141.6h-108c-8.8 56.9-25.6 107.8-50 141.6zM19.3 352c28.6 67.9 86.5 120.4 158 141.6-24.4-33.8-41.2-84.7-50-141.6h-108z"></path></svg> developer.ibm.com/tutorials/l-linux-shells</span></div>

---

background-image: url("figs/02.png")
background-size: 95%
background-position: 50% 10%

---

## .Large[Bourne again shell]

![](https://miro.medium.com/max/1080/1*v4o2AXLIJaHSZmqYZk26qA.jpeg)

---

## .LARGE[.orange[Directory structure and `Bash`]]

---

## .Large[Directory structure]

<div id="htmlwidget-3b237a1000406b6c760e" style="width:100%;height:60%;" class="DiagrammeR html-widget "></div>
<script type="application/json" data-for="htmlwidget-3b237a1000406b6c760e">{"x":{"diagram":"\ngraph TD\nclassDef style_main_node fill:orange,stroke:#333,stroke-width:0px;\nclassDef style_sub_node fill:lightgray,stroke:#333,stroke-width:0px;\n\n A(/) --> B1(home)\n A --> B2(bin)\n A --> B3(etc)\n A --> B4(mnt)\n B1 --> C1(User1)\n B1 --> C2(User2)\n B1 --> C3(User3)\n B2 --> C4(App1)\n B2 --> C5(App1)\n\nclass A style_main_node;\nclass B1,B2,B3,B4,C1,C2,C3,C4,C5 style_sub_node;\n"},"evals":[],"jsHooks":[]}</script>

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>`Bash`</b>] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

## .Large[Linux command-line has a structure]
<br><br>
.content-box-yellow[
.LARGE[**student@biodocker:~$**]
]

---

## .Large[Linux command-line has a structure]
<br><br>

.left[
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;.content-box-grey[.Large[.orange[**PROMPT**]]]  &emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp; .content-box-grey[.Large[.blue[**`ls`**]]] &emsp;&emsp;&emsp;&emsp; .content-box-grey[.Large[.green[**`-l`**]]]&emsp;&emsp;&emsp;&emsp;&emsp; .content-box-grey[.Large[.red[**`/`**]]]
]

--
<br>
<br>

---

## .Large[.center[Exercise]]

Enter into the `Docker` container. .blue[`./login_student.sh`]

List the files. .blue[`ls`]

Change directory to root using `cd` command. .blue[`cd /`]

Display the content of root. .blue[`ls`]

Look for help for `ls` command using option `--help`. .blue[`ls --help`]

Display the content in "long listing format". .blue[`ls -l`]

Display the content in "long listing format" + "sort by modification time". .blue[`ls -l -t`]

Display the content in "long listing format" + "sort by modification time" + "reverse the order of sorting". .blue[`ls -l -t -r`]

Print the working directory using `pwd` command. .blue[`pwd`]

Check your user name by `whoami` command. .blue[`whoami`]

_.blue[.center[.Large[**Most command names are abbreviations of their function.**]]]_

---

background-image: url("figs/03.png")
background-size: 70%
background-position: 50% 80%

## .Large[Path to navigate]

---

background-image: url("figs/04.png")
background-size: 70%
background-position: 50% 80%

## .Large[Path to navigate]

---

## .Large[.center[Some important symbols/ commands]]

<br>

.large[
| Symbols/ Commands  | Descriptions |
| ------------- | ------------- |
| **`.`** | current directory |
| **`..`** | directory up in heirarchy |
| **`cd`** or **`cd ~`** or **`cd ~/`**|  change directory to home directory |
]

---

## .Large[.center[Some important symbols/ commands]]

.large[
| Symbols/ Commands  | Descriptions |
| ------------- | ------------- |
| **`touch`** | create a file |
| **`*`** | list out all the files |
| List**`?`** | any file that begins with List followed by 1 character |
]

---

## .Large[.center[Exercise]]

.content-box-red[
.large[
**Make a folder in your home directory: test. Enter into the test folder. Create some files using `touch` command: test1.txt, test2.txt, abc.txt, DEF.txt, 1file.txt, and bcd.txt. Display all files, display all test files using `?`, and display files starting with a.**
]
]

```bash
cd ~/ # go to home directory

mkdir test # make a test directory

cd test # change directory

touch test1.txt test2.txt abc.txt DEF.txt 1file.txt bcd.txt # create files

ls # display all files

ls test?.txt # display all test files

ls a* # display all files starting with a

```
---

## .Large[.center[Some important symbols/ commands]]

.large[
| Symbols/ Commands  | Descriptions |
| ------------- | ------------- |
| **`[`**abc**`]*`** | any file that begins with either ‘a’ or ‘b’ or ‘c’ and ending with any number of characters |
| **`[[:upper:]]*`** | any file that begins with an uppercase letter |
| **`[![:upper:]]*`** | any file that does notbegins with an uppercase letter |
| **`[[:digit:]]*`** | any file that begins with digit |
| **`[![:digit:]]*`** | any file that does not begins with digit |
| **`[`**a-d**`]???`** | any file that begins from a range of a-d and followed by exactly 3 character |
]

---

## .Large[.center[Some important symbols/ commands]]

<br>

.large[
| Symbols/ Commands  | Descriptions |
| ------------- | ------------- |
| **`echo`** | display argument |
| **`$*`** | stored variables |
| **`history`** | display history of your activity |
]

---

## .Large[.center[Exercise]]

.content-box-red[
.large[
**Print "Hello World!". Store "Hello World!" in a varaible named `hello`. Display the history of your activity.**
]
]

```bash
echo "Hello World!" # print

hello="Hello World!" # store into a variable
echo $hello # print content of variable

history # display history of your activity
```
---

## .Large[.center[Some important symbols/ commands]]

.large[
| Symbols/ Commands  | Descriptions |
| ------------- | ------------- |
| **`mkdir`** | make a directory |
| **`rmdir`** | remove a directory |
| **`rm`** | remove  files/ directories |
| **`cp`** | copy files/ directories |
| **`mv`** | move  files/ directories |
| **`wget`** | download file from internet |
]

---

## .Large[.center[Some important symbols/ commands]]

.large[
| Symbols/ Commands  | Descriptions |
| ------------- | ------------- |
| **`less`, `more`, `head`, `tail`, `cat`** | show content |
| **`grep`, `cut`, `uniq`, `sort`** | search or extract or modify or sort |
| **`tr`** | string manipulation |
| **`wc`** | count |
]

<br>

.content-box-red[
.Large[
**[arabidopsis.org/download_files/Genes/TAIR10_genome_release/
TAIR10_gff3/TAIR10_GFF3_genes.gff](https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff)**
]
]

---

## .LARGE[.orange[Redirection]]

---

background-image: url("https://res.cloudinary.com/practicaldev/image/fetch/s--6BUHx0iu--/c_limit%2Cf_auto%2Cfl_progressive%2Cq_auto%2Cw_880/https://miro.medium.com/max/2400/1%2Ay3_tArgpKbZp1CiR5MpKeg.png")
background-size: 60%
background-position: 50% 80%

## .Large[.center[STDIN, STDOUT, and STDERR]]

---

background-image: url("https://upload.wikimedia.org/wikipedia/commons/f/f6/Pipeline.svg")
background-size: 45%
background-position: 50% 80%

## .Large[.center[STDIN, STDOUT, and STDERR]]

---

class: center,hide_logo
background-image: url("https://miro.medium.com/proxy/1*vnibgmWDDM6ay-WQMyrQnQ.png")
background-size: contain
background-position: 50% 50%

## .Large[Pipes]

---

## .Large[.center[Redirection]]
<br>

.Large[
| Symbols/ Commands  | Descriptions |
| ------------- | ------------- |
| **`>`** | Standard output redirection|
| **`<`** | Standard Input redirection|
| **`2>`** | Standard error redirection|
| **`&>`** | Standard output and error redirection|
| **`>>`** | Standard output redirection|
| **`<<`** | Standard input redirection|
| <b>&#x7c;</b> | Redirection using pipes |
]

---

## .LARGE[.orange[`Bash` scripting]]

---

## .Large[.center[Text editors]]

<br>

- .LARGE[`nano`]

- .LARGE[`vim`]

- .LARGE[`emacs`]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

## .Large[.center[Bash scripts]]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

# This script will print ...

echo "Hello World!"
```
]

# a comment

# code
```
]

# This script will print my name

name="Deepak Tanwar"

echo "Hello $name!"
```
]

# a comment

# store name in a variable

# print name
```
]

---

## .Large[.center[Bash script]]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

```bash
nano name.sh # create a file using nano

#!/bin/bash
echo "Deepak Tanwar"

# close the file with ctrl + x
```

```bash
bash name.sh > name.stdout
```
---

## .Large[.center[Bash script]]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

```bash
bash name.sh 2> name.stderr
```

--
.content-box-red[
**Append `name.stdout` with your favourite animal.**
]

```bash
echo "Tiger" >> name.stdout
```
---

## .Large[.center[Bash script]]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

```bash
echo "Fondue" 2>> name.stderr
```

---

background-image: url("figs/06.png")
background-size: 70%
background-position: 50% 80%

## .Large[Flow control]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

background-image: url("figs/07.png")
background-size: 70%
background-position: 50% 80%

## .Large[`for` loop]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

background-image: url("figs/08.png")
background-size: 70%
background-position: 50% 80%

## .Large[`for` loop]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

background-image: url("figs/09.png")
background-size: 70%
background-position: 50% 80%

## .Large[`while` loop]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

background-image: url("figs/10.png")
background-size: 60%
background-position: 50% 80%

## .Large[if-else]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

background-image: url("figs/11.png")
background-size: 70%
background-position: 50% 80%

## .Large[if-else]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Scripting</b>] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

## .LARGE[.orange[Setting path and permissions]]

---

## .Large[.center[Setting path]]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Permissions</b>] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

<br>
```bash
export PATH="/path/to/dir:$PATH"
```
<br>

```bash
export PATH="/path/to/dir:$PATH" >> ~/.bash_profile
```

<br>

```bash
export PATH="/path/to/dir:$PATH" >> ~/.bashrc
```

---

background-image: url("figs/12.png")
background-size: 100%
background-position: 50% 80%

## .Large[Permissions and changing permissions]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Permissions</b>] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>
---

background-image: url("figs/13.png")
background-size: 70%
background-position: 50% 80%

## .Large[Permissions and changing permissions]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Permissions</b>] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

background-image: url("figs/14.png")
background-size: 90%
background-position: 50% 90%

## .Large[Permissions and changing permissions]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Permissions</b>] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

---

## .Large[.center[Power of `&&`]]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Permissions</b>] </div>
<div class="my-footer5" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Exercise] </div>

.Large[Do a **task2** only after **task1** is completed]

### Not working example
```bash
echo "Hello"; echo "World"
```

### Working example
```bash
echo "Hello" && echo "World"
```

---

## .LARGE[.orange[Testing your knowledge]]

---

## .Large[Problem 1]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Exercise</b>] </div>

.large[
PFAM is a domain database. It also includes domains that have already been computed for all proteomes. The most recent version is available here: [https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam35.0/proteomes/](https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam35.0/proteomes/). Each file represents a proteome, which is recognized by its taxonomy ID. The ID `9606` belongs to a human. Each of these files is tab-delimited, with the domain ID in the sixth column. Using `wget`, download the human proteome file. After downloading, run a single line of `bash` commands to determine the number of domain types (unique domains) in the human genome. You may use as many commands as you want, connected together in `pipes`.
]

---

## .Large[Problem 2]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Exercise</b>] </div>

.large[
Download the covid19 fasta file from [https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam_SARS-CoV-2_2.0/](https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam_SARS-CoV-2_2.0/) using `wget` command.

1. How many proteins are there?
2. How many amino acids are there?
3. Take only the protein sequences, and convert them to lower case.
]

--
<br>

```perl
cat covid-19.fasta | grep ">" | wc -l
```

```perl
cat covid-19.fasta | grep -v ">" | wc -c
```

```perl
cat covid-19.fasta | grep -v ">" | tr [:upper:] [:lower:]
```

---

## .Large[Problem 3]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Exercise</b>] </div>

1. Make a directory in your home folder `software/bin`.
2. Change directory to `software/bin`.
3. Write a `bash` script that take an input: taxonomy ID.
4. If file does not exist, Script should download the proteome file for the input taxonomy ID.
5. Script should run a single line of `bash` commands to determine the number of domain types (unique domains) in the genome.
6. Run step 5 **only if** step 4 is finished.
7. Save your file as `count_uniq_domains`
8. Add your script to `PATH`
9. Go to your home folder.
10. Create a `bash` script that will run `count_uniq_domains` (without specifying path). This script should store `STDOUT` and `STDERR`.
]

---

## .Large[Problem 3]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Exercise</b>] </div>

```bash
# 1 and 2

cd ~/
mkdir software
cd software
mkdir bin
```

```bash
# 3, 4, 5, 6, and 7

nano count_uniq_domains

#!/bin/bash

txid=$1
txid2=$txid.final.tsv.gz

---

## .Large[Problem 3]

<div class="my-footer1" style="text-align: center;background-color:#D9D9D9;"> .grey[Background] </div>
<div class="my-footer2" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[`Bash`] </div>
<div class="my-footer3" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Scripting] </div>
<div class="my-footer4" style="text-align: center;background-color:#D9D9D9;border-left:1px solid black;"> .grey[Permissions] </div>
<div class="my-footer5" style="text-align: center;background-color:#FEE0D2;border-left:1px solid black;"> .blue[<b>Exercise</b>] </div>

```bash
# 8

chmod +x count_uniq_domains

export PATH="~/software/bin/:$PATH"
```

```bash
# 9

cd ~/
```

```bash
# 10

nano run.sh

#!/bin/bash

count_uniq_domains 9696 > STDOUT 2>STDERR

## close the file with ctrl + x

bash run.sh
```

---

## Resources

https://github.com/urppeia/BIO609_2016

https://github.com/urppeia/BIO609_2017

https://github.com/urppeia/BIO609_2018

https://github.com/urppeia/bio609

https://github.com/urppeia/BIO609_2021

---

background-image: url("figs/bitly.png")
background-size: 45%
background-position: 50% 40%

## Instructor and Course evaluation

<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
.content-box-green[.blue[.LARGE[[bit.ly/bio609_2023](https://bit.ly/bio609_2023)]]]

---