Introduction to the Command Line (Terminal)

Gepoliano Chaves, Ph. D.

September 9th, 2023

0) Git clone GitHub repository in the VM Desktop

This command should be entered at the terminal in your Virtual Machine.

git clone https://github.com/gepolianochaves/bioinformatics-bridge-course

1. Introducing the Shell

print working directory

pwd

## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts

list

ls

## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder

1. Introducing the Shell (continued)

command not found

pws

2. Navigating files and directories

pwd

## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts

Indicate directory with slash and file without slash

ls -F

## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder/

2. Navigating files and directories (continued)

Getting help

ls --help

Read the manual of the command

man ls

2. Navigating files and directories (continued)

Move to different directory

cd ../
ls

## data
## figures
## scripts

2. Navigating files and directories (continued)

 ls -F -a

## ./
## ../
## .DS_Store
## .Rhistory
## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder/

2. Navigating files and directories (continued)

move to the Desktop folder

cd ~/Desktop
ls

## 2021-02-10CAPES template - Laspau Confirmation of Funding Gepoliano Dos Santos Chaves.pdf
## AcessoInfi_SEI_23038.009779_2016_72.pdf
## English
## Gepoliano
## Gepoliano Desktop Backup
## Hazards Risk.pdf
## Kitanaka 2002.pdf
## Liu, Skapek.pdf
## Screen Shot 2023-08-19 at 2.51.03 PM.png
## Screen Shot 2023-08-19 at 4.27.02 PM.png
## Screen Shot 2023-09-01 at 7.50.06 PM.png
## Screen Shot 2023-09-05 at 7.57.59 PM.png
## Screen Shot 2023-09-06 at 8.03.09 PM.png
## Zhang, 2023.pdf
## cisco-secure-client-macos-5.0.03072-predeploy-k9.dmg
## contacts.xlsx
## ~$Cox.docx
## ~$ansportation Consent.docx
## ~$contacts.xlsx
## ~$r Angela.docx

2. Navigating files and directories (continued)

Absolute vs. Relative Paths

A system path.

2. Navigating files and directories (continued)

General syntax of the shell command

A system path.

3. Working With Files and Directories

Create a directory using the mkdir command

mkdir -p thesis

3. Working With Files and Directories (continued)

List the files in the current directory. If the option -a is included, folders are included as well

ls -F -a

## ./
## ../
## .DS_Store
## .Rhistory
## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder/
## thesis/

3. Working With Files and Directories (continued)

Let’s check what is the current directory and change our working directory to test using cd
Then run a text editor called Touch to create a file called draft.txt.
Finally, we will check that we created the file with the ls command:

3. Working With Files and Directories (continued)

pwd
cd thesis
touch draft.txt
ls

## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts
## draft.txt

3. Working With Files and Directories (continued)

Let’s go back to the scripts folder

# check the current directory
pwd
# change to the test directory
cd ./thesis
# check the current directory
pwd
# change to the scripts directory
cd ../
# check the current directory
pwd

## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts
## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts/thesis
## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts

3. Working With Files and Directories (continued)

# check the current directory
pwd
# Move draft.txt to current directory
mv ./thesis/draft.txt ./
# List current directory
ls
# Move draft.txt back to ./thesis
mv draft.txt ./thesis/
# change to thesis directory 
cd ./thesis
# List current directory and confirm draft there
ls

## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts
## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## draft.txt
## test folder
## thesis
## draft.txt

3. Working With Files and Directories (continued)

Removing files and directories

ls ./thesis/draft.txt
rm ./thesis/draft.txt
ls ./thesis/draft.txt
ls ./thesis/
du -sh ./thesis/

## ./thesis/draft.txt
## ls: ./thesis/draft.txt: No such file or directory
##   0B ./thesis/

3. Working With Files and Directories (continued)

Removing the thesis directory

ls
echo "Not using the -r option:"
rm thesis
ls

## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder
## thesis
## Not using the -r option:
## rm: thesis: is a directory
## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder
## thesis

3. Working With Files and Directories (continued)

ls
echo "Using the -r option:"
rm -r thesis
ls

## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder
## thesis
## Using the -r option:
## Introduction to R and Terminal.Rmd
## Introduction to the Terminal.Rmd
## Introduction-to-R-and-Terminal.html
## Introduction-to-the-Terminal.Rmd
## Introduction-to-the-Terminal.html
## test folder

4. Pipes and Filters

wc counts lines, words, and characters in its inputs.
cat displays the contents of its inputs.
sort sorts its inputs.
head displays the first 10 lines of its input.

4. Pipes and Filters (continued)

tail displays the last 10 lines of its input.
command > [file] redirects a command’s output to a file (overwriting any existing content).
command >> [file] appends a command’s output to a file.
[first] | [second] is a pipeline: the output of the first command is used as the input to the second.
The best way to use the shell is to use pipes to combine simple single-purpose programs (filters).

5. Loops

Let’s count how many FASTA files are there in the fasta folder of the brazil region for 2020
We will use a for loop used in the
We will come across this again in the Variant Call Pipeline that we will study

5. Loops (continued)

Print the names of every FASTA file.

cd ../../2-Variant-Call-Pipeline/regions/brazil/2020/fasta
for i in Brazil*; do echo $i; done

## Brazil_2020_07_01-2020_12_31_1.fasta
## Brazil_2020_07_01-2020_12_31_10.fasta
## Brazil_2020_07_01-2020_12_31_100.fasta
## Brazil_2020_07_01-2020_12_31_101.fasta
## Brazil_2020_07_01-2020_12_31_102.fasta
## Brazil_2020_07_01-2020_12_31_103.fasta
## Brazil_2020_07_01-2020_12_31_104.fasta
## Brazil_2020_07_01-2020_12_31_105.fasta
## Brazil_2020_07_01-2020_12_31_106.fasta
## Brazil_2020_07_01-2020_12_31_107.fasta
## Brazil_2020_07_01-2020_12_31_108.fasta
## Brazil_2020_07_01-2020_12_31_109.fasta
## Brazil_2020_07_01-2020_12_31_11.fasta
## Brazil_2020_07_01-2020_12_31_110.fasta
## Brazil_2020_07_01-2020_12_31_111.fasta
## Brazil_2020_07_01-2020_12_31_112.fasta
## Brazil_2020_07_01-2020_12_31_113.fasta
## Brazil_2020_07_01-2020_12_31_114.fasta
## Brazil_2020_07_01-2020_12_31_115.fasta
## Brazil_2020_07_01-2020_12_31_116.fasta
## Brazil_2020_07_01-2020_12_31_117.fasta
## Brazil_2020_07_01-2020_12_31_118.fasta
## Brazil_2020_07_01-2020_12_31_119.fasta
## Brazil_2020_07_01-2020_12_31_12.fasta
## Brazil_2020_07_01-2020_12_31_120.fasta
## Brazil_2020_07_01-2020_12_31_121.fasta
## Brazil_2020_07_01-2020_12_31_122.fasta
## Brazil_2020_07_01-2020_12_31_123.fasta
## Brazil_2020_07_01-2020_12_31_124.fasta
## Brazil_2020_07_01-2020_12_31_125.fasta
## Brazil_2020_07_01-2020_12_31_126.fasta
## Brazil_2020_07_01-2020_12_31_127.fasta
## Brazil_2020_07_01-2020_12_31_128.fasta
## Brazil_2020_07_01-2020_12_31_129.fasta
## Brazil_2020_07_01-2020_12_31_13.fasta
## Brazil_2020_07_01-2020_12_31_130.fasta
## Brazil_2020_07_01-2020_12_31_131.fasta
## Brazil_2020_07_01-2020_12_31_132.fasta
## Brazil_2020_07_01-2020_12_31_133.fasta
## Brazil_2020_07_01-2020_12_31_134.fasta
## Brazil_2020_07_01-2020_12_31_135.fasta
## Brazil_2020_07_01-2020_12_31_136.fasta
## Brazil_2020_07_01-2020_12_31_137.fasta
## Brazil_2020_07_01-2020_12_31_138.fasta
## Brazil_2020_07_01-2020_12_31_139.fasta
## Brazil_2020_07_01-2020_12_31_14.fasta
## Brazil_2020_07_01-2020_12_31_140.fasta
## Brazil_2020_07_01-2020_12_31_141.fasta
## Brazil_2020_07_01-2020_12_31_142.fasta
## Brazil_2020_07_01-2020_12_31_143.fasta
## Brazil_2020_07_01-2020_12_31_144.fasta
## Brazil_2020_07_01-2020_12_31_145.fasta
## Brazil_2020_07_01-2020_12_31_146.fasta
## Brazil_2020_07_01-2020_12_31_147.fasta
## Brazil_2020_07_01-2020_12_31_148.fasta
## Brazil_2020_07_01-2020_12_31_149.fasta
## Brazil_2020_07_01-2020_12_31_15.fasta
## Brazil_2020_07_01-2020_12_31_150.fasta
## Brazil_2020_07_01-2020_12_31_151.fasta
## Brazil_2020_07_01-2020_12_31_152.fasta
## Brazil_2020_07_01-2020_12_31_153.fasta
## Brazil_2020_07_01-2020_12_31_154.fasta
## Brazil_2020_07_01-2020_12_31_155.fasta
## Brazil_2020_07_01-2020_12_31_156.fasta
## Brazil_2020_07_01-2020_12_31_157.fasta
## Brazil_2020_07_01-2020_12_31_158.fasta
## Brazil_2020_07_01-2020_12_31_159.fasta
## Brazil_2020_07_01-2020_12_31_16.fasta
## Brazil_2020_07_01-2020_12_31_160.fasta
## Brazil_2020_07_01-2020_12_31_161.fasta
## Brazil_2020_07_01-2020_12_31_162.fasta
## Brazil_2020_07_01-2020_12_31_163.fasta
## Brazil_2020_07_01-2020_12_31_164.fasta
## Brazil_2020_07_01-2020_12_31_165.fasta
## Brazil_2020_07_01-2020_12_31_166.fasta
## Brazil_2020_07_01-2020_12_31_167.fasta
## Brazil_2020_07_01-2020_12_31_168.fasta
## Brazil_2020_07_01-2020_12_31_169.fasta
## Brazil_2020_07_01-2020_12_31_17.fasta
## Brazil_2020_07_01-2020_12_31_170.fasta
## Brazil_2020_07_01-2020_12_31_171.fasta
## Brazil_2020_07_01-2020_12_31_172.fasta
## Brazil_2020_07_01-2020_12_31_173.fasta
## Brazil_2020_07_01-2020_12_31_174.fasta
## Brazil_2020_07_01-2020_12_31_175.fasta
## Brazil_2020_07_01-2020_12_31_176.fasta
## Brazil_2020_07_01-2020_12_31_177.fasta
## Brazil_2020_07_01-2020_12_31_178.fasta
## Brazil_2020_07_01-2020_12_31_179.fasta
## Brazil_2020_07_01-2020_12_31_18.fasta
## Brazil_2020_07_01-2020_12_31_180.fasta
## Brazil_2020_07_01-2020_12_31_181.fasta
## Brazil_2020_07_01-2020_12_31_182.fasta
## Brazil_2020_07_01-2020_12_31_183.fasta
## Brazil_2020_07_01-2020_12_31_184.fasta
## Brazil_2020_07_01-2020_12_31_185.fasta
## Brazil_2020_07_01-2020_12_31_186.fasta
## Brazil_2020_07_01-2020_12_31_187.fasta
## Brazil_2020_07_01-2020_12_31_188.fasta
## Brazil_2020_07_01-2020_12_31_189.fasta
## Brazil_2020_07_01-2020_12_31_19.fasta
## Brazil_2020_07_01-2020_12_31_190.fasta
## Brazil_2020_07_01-2020_12_31_191.fasta
## Brazil_2020_07_01-2020_12_31_192.fasta
## Brazil_2020_07_01-2020_12_31_193.fasta
## Brazil_2020_07_01-2020_12_31_194.fasta
## Brazil_2020_07_01-2020_12_31_195.fasta
## Brazil_2020_07_01-2020_12_31_196.fasta
## Brazil_2020_07_01-2020_12_31_197.fasta
## Brazil_2020_07_01-2020_12_31_198.fasta
## Brazil_2020_07_01-2020_12_31_199.fasta
## Brazil_2020_07_01-2020_12_31_2.fasta
## Brazil_2020_07_01-2020_12_31_20.fasta
## Brazil_2020_07_01-2020_12_31_200.fasta
## Brazil_2020_07_01-2020_12_31_201.fasta
## Brazil_2020_07_01-2020_12_31_202.fasta
## Brazil_2020_07_01-2020_12_31_203.fasta
## Brazil_2020_07_01-2020_12_31_204.fasta
## Brazil_2020_07_01-2020_12_31_205.fasta
## Brazil_2020_07_01-2020_12_31_206.fasta
## Brazil_2020_07_01-2020_12_31_207.fasta
## Brazil_2020_07_01-2020_12_31_208.fasta
## Brazil_2020_07_01-2020_12_31_209.fasta
## Brazil_2020_07_01-2020_12_31_21.fasta
## Brazil_2020_07_01-2020_12_31_210.fasta
## Brazil_2020_07_01-2020_12_31_211.fasta
## Brazil_2020_07_01-2020_12_31_212.fasta
## Brazil_2020_07_01-2020_12_31_213.fasta
## Brazil_2020_07_01-2020_12_31_214.fasta
## Brazil_2020_07_01-2020_12_31_215.fasta
## Brazil_2020_07_01-2020_12_31_216.fasta
## Brazil_2020_07_01-2020_12_31_217.fasta
## Brazil_2020_07_01-2020_12_31_218.fasta
## Brazil_2020_07_01-2020_12_31_219.fasta
## Brazil_2020_07_01-2020_12_31_22.fasta
## Brazil_2020_07_01-2020_12_31_220.fasta
## Brazil_2020_07_01-2020_12_31_221.fasta
## Brazil_2020_07_01-2020_12_31_222.fasta
## Brazil_2020_07_01-2020_12_31_223.fasta
## Brazil_2020_07_01-2020_12_31_224.fasta
## Brazil_2020_07_01-2020_12_31_225.fasta
## Brazil_2020_07_01-2020_12_31_226.fasta
## Brazil_2020_07_01-2020_12_31_227.fasta
## Brazil_2020_07_01-2020_12_31_228.fasta
## Brazil_2020_07_01-2020_12_31_229.fasta
## Brazil_2020_07_01-2020_12_31_23.fasta
## Brazil_2020_07_01-2020_12_31_230.fasta
## Brazil_2020_07_01-2020_12_31_231.fasta
## Brazil_2020_07_01-2020_12_31_232.fasta
## Brazil_2020_07_01-2020_12_31_233.fasta
## Brazil_2020_07_01-2020_12_31_234.fasta
## Brazil_2020_07_01-2020_12_31_235.fasta
## Brazil_2020_07_01-2020_12_31_236.fasta
## Brazil_2020_07_01-2020_12_31_237.fasta
## Brazil_2020_07_01-2020_12_31_238.fasta
## Brazil_2020_07_01-2020_12_31_239.fasta
## Brazil_2020_07_01-2020_12_31_24.fasta
## Brazil_2020_07_01-2020_12_31_240.fasta
## Brazil_2020_07_01-2020_12_31_241.fasta
## Brazil_2020_07_01-2020_12_31_242.fasta
## Brazil_2020_07_01-2020_12_31_243.fasta
## Brazil_2020_07_01-2020_12_31_244.fasta
## Brazil_2020_07_01-2020_12_31_245.fasta
## Brazil_2020_07_01-2020_12_31_246.fasta
## Brazil_2020_07_01-2020_12_31_247.fasta
## Brazil_2020_07_01-2020_12_31_248.fasta
## Brazil_2020_07_01-2020_12_31_249.fasta
## Brazil_2020_07_01-2020_12_31_25.fasta
## Brazil_2020_07_01-2020_12_31_250.fasta
## Brazil_2020_07_01-2020_12_31_26.fasta
## Brazil_2020_07_01-2020_12_31_27.fasta
## Brazil_2020_07_01-2020_12_31_28.fasta
## Brazil_2020_07_01-2020_12_31_29.fasta
## Brazil_2020_07_01-2020_12_31_3.fasta
## Brazil_2020_07_01-2020_12_31_30.fasta
## Brazil_2020_07_01-2020_12_31_31.fasta
## Brazil_2020_07_01-2020_12_31_32.fasta
## Brazil_2020_07_01-2020_12_31_33.fasta
## Brazil_2020_07_01-2020_12_31_34.fasta
## Brazil_2020_07_01-2020_12_31_35.fasta
## Brazil_2020_07_01-2020_12_31_36.fasta
## Brazil_2020_07_01-2020_12_31_37.fasta
## Brazil_2020_07_01-2020_12_31_38.fasta
## Brazil_2020_07_01-2020_12_31_39.fasta
## Brazil_2020_07_01-2020_12_31_4.fasta
## Brazil_2020_07_01-2020_12_31_40.fasta
## Brazil_2020_07_01-2020_12_31_41.fasta
## Brazil_2020_07_01-2020_12_31_42.fasta
## Brazil_2020_07_01-2020_12_31_43.fasta
## Brazil_2020_07_01-2020_12_31_44.fasta
## Brazil_2020_07_01-2020_12_31_45.fasta
## Brazil_2020_07_01-2020_12_31_46.fasta
## Brazil_2020_07_01-2020_12_31_47.fasta
## Brazil_2020_07_01-2020_12_31_48.fasta
## Brazil_2020_07_01-2020_12_31_49.fasta
## Brazil_2020_07_01-2020_12_31_5.fasta
## Brazil_2020_07_01-2020_12_31_50.fasta
## Brazil_2020_07_01-2020_12_31_51.fasta
## Brazil_2020_07_01-2020_12_31_52.fasta
## Brazil_2020_07_01-2020_12_31_53.fasta
## Brazil_2020_07_01-2020_12_31_54.fasta
## Brazil_2020_07_01-2020_12_31_55.fasta
## Brazil_2020_07_01-2020_12_31_56.fasta
## Brazil_2020_07_01-2020_12_31_57.fasta
## Brazil_2020_07_01-2020_12_31_58.fasta
## Brazil_2020_07_01-2020_12_31_59.fasta
## Brazil_2020_07_01-2020_12_31_6.fasta
## Brazil_2020_07_01-2020_12_31_60.fasta
## Brazil_2020_07_01-2020_12_31_61.fasta
## Brazil_2020_07_01-2020_12_31_62.fasta
## Brazil_2020_07_01-2020_12_31_63.fasta
## Brazil_2020_07_01-2020_12_31_64.fasta
## Brazil_2020_07_01-2020_12_31_65.fasta
## Brazil_2020_07_01-2020_12_31_66.fasta
## Brazil_2020_07_01-2020_12_31_67.fasta
## Brazil_2020_07_01-2020_12_31_68.fasta
## Brazil_2020_07_01-2020_12_31_69.fasta
## Brazil_2020_07_01-2020_12_31_7.fasta
## Brazil_2020_07_01-2020_12_31_70.fasta
## Brazil_2020_07_01-2020_12_31_71.fasta
## Brazil_2020_07_01-2020_12_31_72.fasta
## Brazil_2020_07_01-2020_12_31_73.fasta
## Brazil_2020_07_01-2020_12_31_74.fasta
## Brazil_2020_07_01-2020_12_31_75.fasta
## Brazil_2020_07_01-2020_12_31_76.fasta
## Brazil_2020_07_01-2020_12_31_77.fasta
## Brazil_2020_07_01-2020_12_31_78.fasta
## Brazil_2020_07_01-2020_12_31_79.fasta
## Brazil_2020_07_01-2020_12_31_8.fasta
## Brazil_2020_07_01-2020_12_31_80.fasta
## Brazil_2020_07_01-2020_12_31_81.fasta
## Brazil_2020_07_01-2020_12_31_82.fasta
## Brazil_2020_07_01-2020_12_31_83.fasta
## Brazil_2020_07_01-2020_12_31_84.fasta
## Brazil_2020_07_01-2020_12_31_85.fasta
## Brazil_2020_07_01-2020_12_31_86.fasta
## Brazil_2020_07_01-2020_12_31_87.fasta
## Brazil_2020_07_01-2020_12_31_88.fasta
## Brazil_2020_07_01-2020_12_31_89.fasta
## Brazil_2020_07_01-2020_12_31_9.fasta
## Brazil_2020_07_01-2020_12_31_90.fasta
## Brazil_2020_07_01-2020_12_31_91.fasta
## Brazil_2020_07_01-2020_12_31_92.fasta
## Brazil_2020_07_01-2020_12_31_93.fasta
## Brazil_2020_07_01-2020_12_31_94.fasta
## Brazil_2020_07_01-2020_12_31_95.fasta
## Brazil_2020_07_01-2020_12_31_96.fasta
## Brazil_2020_07_01-2020_12_31_97.fasta
## Brazil_2020_07_01-2020_12_31_98.fasta
## Brazil_2020_07_01-2020_12_31_99.fasta

5. Loops (continued)

Let’s pipe this output into the wc command and let’s have it count how many files, for us.

cd ../../2-Variant-Call-Pipeline/regions/brazil/2020/fasta
for i in Brazil*; do echo $i; done | wc

##      250     250    9642

Now count only the number of lines

cd ../../2-Variant-Call-Pipeline/regions/brazil/2020/fasta
for i in Brazil*; do echo $i; done | wc -l

##      250

6. Shell Scripts

Variant call shell script: an alignment in a for loop


Region=brazil

for fasta_file in $(cat brazil_fasta_julDec/COVID_List_Region.txt); do 

  ## Print names of Project Directory and FASTA file
  echo $ProjectDirectory
  echo $fast_file
  
  
  ## Alignment
  ~/anaconda3/bin/bwa mem -M -R \
  '@RG\tID:SampleCorona\tLB:sample_1\tPL:ILLUMINA\tPM:HISEQ\tSM:SampleCorona' \
  fasta_reference_file/SARS-CoV-2.fasta \
  brazil_fasta_julDec/$fasta_file > \
  brazil_alignment_julDec_sam/$fasta_file".sam"
  
  
  ## SAM to BAM
  samtools view -S -b $Region"_alignment_julDec_sam"/$fasta_file".sam" > \
  $Region"_alignment_julDec_bam"/$fasta_file".bam"
  
  
  ## Samtools uses reference FASTA to detect "piles" in the alignment
  samtools mpileup -g -f fasta_reference_file/SARS-CoV-2.fasta $Region"_alignment_julDec_bam"/$fasta_file".bam" > \
  $Region"_julDec_bcf"/$fasta_file".bcf"
  
  ## Bcftools extracts SNPs
  ~/Desktop/Gepoliano/bcftools/bcftools view -v snps $Region"_julDec_bcf"/$fasta_file".bcf" > $Region"_vcf_julDec_snp"/$fasta_file"_snps.vcf"

  ## Bcftools extracts indels
  ~/Desktop/Gepoliano/bcftools/bcftools view -v indels $Region"_julDec_bcf"/$fasta_file".bcf" > $Region"_vcf_julDec_indel"/$fasta_file"_indels.vcf"

done

7. Finding Things

The find command

pwd
find . -name "*Rmd" -print

## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts
## ./Introduction to the Terminal.Rmd
## ./Introduction-to-the-Terminal.Rmd
## ./Introduction to R and Terminal.Rmd

find names of figures of format png

pwd
find ../figures -name "*png" -print

## /Users/gepolianochaves/Desktop/Gepoliano/SIP2023_BME03/recombio/1-Introduction/scripts
## ../figures/general syntax.png
## ../figures/absolute vs relative paths.png

7. Finding Things (continued)

The grep command

grep "print" Introduction\ to\ the\ Terminal.Rmd

##   #   df_print: paged
## print working directory
## find . -name "*Rmd" -print
## find ../figures -name "*png" -print
## grep "print" Introduction\ to\ the\ Terminal.Rmd

7. Finding Things (continued)

The cat and head commands

cat Introduction\ to\ the\ Terminal.Rmd | head

## ---
## title: "Introduction to the Command Line (Terminal)"
## author: "Gepoliano Chaves, Ph. D."
## date: "September 9th, 2023"
## output:
##   # pdf_document: default
##   # output: slidy_presentation
##   revealjs::revealjs_presentation
##   # html_document:
##   #   df_print: paged

8) References

9) Session Info

sessionInfo()

## R version 4.1.1 (2021-08-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] revealjs_0.9    digest_0.6.32   R6_2.5.1        jsonlite_1.8.7 
##  [5] evaluate_0.21   cachem_1.0.8    rlang_1.1.1     cli_3.6.1      
##  [9] rstudioapi_0.14 jquerylib_0.1.4 bslib_0.5.0     rmarkdown_2.22 
## [13] tools_4.1.1     xfun_0.39       yaml_2.3.7      fastmap_1.1.1  
## [17] compiler_4.1.1  htmltools_0.5.5 knitr_1.43      sass_0.4.6