Working with Unix

File and directory navigation

pwd   Print working direcoory
ls    List files
mkdir Make directory
rmdir Remove directory
cd    Change directory
rm    Remove file
touch Create empty file
cp    Copy file
mv    Move file

Where am I?

[1]:

pwd

/home/jovyan/work/Duke_HTS2019/cliburn

List files

[2]:

ls

data
figs
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

[3]:

ls -a

.
..
data
figs
.gitignore
.ipynb_checkpoints
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

[4]:

ls -l

total 4680
drwxr-xr-x 2 jovyan users    4096 Jun 25 15:34 data
drwxr-xr-x 2 jovyan users    4096 Jun 26 08:52 figs
-rw-r--r-- 1 jovyan users   20314 Jun 26 08:42 R00_Review_Basics.ipynb
-rw-r--r-- 1 jovyan users    2889 Jun 25 15:34 R00_Review_Basics_Scratch.ipynb
-rw-r--r-- 1 jovyan users   10478 Jun 25 15:34 R01_Data_Manipulation.ipynb
-rw-r--r-- 1 jovyan users    7169 Jun 25 15:34 R01_Data_Manipulation_Scratch.ipynb
-rw-r--r-- 1 jovyan users  119305 Jun 26 08:43 R01_Data_Manipulation_Solutions.ipynb
-rw-r--r-- 1 jovyan users    3535 Jun 25 15:34 R01_Manipulating_Data_In_R.ipynb
-rw-r--r-- 1 jovyan users   40260 Jun 25 15:34 R02_Tidying_Data_In_R.ipynb
-rw-r--r-- 1 jovyan users    4912 Jun 25 15:34 R02_Tidying_Data.ipynb
-rw-r--r-- 1 jovyan users   64595 Jun 26 08:45 R02_Tidying_Data_Solutions.ipynb
-rw-r--r-- 1 jovyan users   23158 Jun 26 08:46 R03_FileIO.ipynb
-rw-r--r-- 1 jovyan users 1207248 Jun 26 08:55 R04_Unsupervised_Learning.ipynb
-rw-r--r-- 1 jovyan users   11822 Jun 25 15:34 R04_Unsupervised_Learning_Scratch.ipynb
-rw-r--r-- 1 jovyan users 1137154 Jun 26 08:55 R05_Unsupervised_Learning_More_Examples.ipynb
-rw-r--r-- 1 jovyan users  157680 Jun 26 08:55 R06_Graphics_Overview.ipynb
-rw-r--r-- 1 jovyan users  214118 Jun 26 08:55 R07_Graphics_Base.ipynb
-rw-r--r-- 1 jovyan users 1394754 Jun 26 08:55 R08_Graphics_ggplot2.ipynb
-rw-r--r-- 1 jovyan users    4931 Jun 26 08:55 R09_Graphics_Exercise.ipynb
-rw-r--r-- 1 jovyan users  104001 Jun 26 08:55 R09_Graphics_Exercise_Solutions.ipynb
drwxr-xr-x 2 jovyan users    4096 Jun 25 15:34 seqs
-rw-r--r-- 1 jovyan users   10940 Jun 25 15:34 Unix01_File_And_Directory.ipynb
-rw-r--r-- 1 jovyan users   21469 Jun 26 09:14 Unix01_File_And_Directory_Solutions.ipynb
-rw-r--r-- 1 jovyan users   11715 Jun 25 15:34 Unix02_FileIO.ipynb
-rw-r--r-- 1 jovyan users   12232 Jun 25 15:34 Unix02_FileIO_Solutions.ipynb
-rw-r--r-- 1 jovyan users    8037 Jun 25 15:34 Unix03_File_Storage.ipynb
-rw-r--r-- 1 jovyan users    8477 Jun 25 15:34 Unix03_File_Storage_Solutions.ipynb
-rw-r--r-- 1 jovyan users   10875 Jun 25 15:34 Unix04_Text_Manipulation.ipynb
-rw-r--r-- 1 jovyan users   11276 Jun 25 15:34 Unix04_Text_Manipulation_Solutinos.ipynb
-rw-r--r-- 1 jovyan users   15609 Jun 25 15:34 Unix05_Variables.ipynb
-rw-r--r-- 1 jovyan users   15609 Jun 25 15:34 Unix05_Variables_Solutions.ipynb
-rw-r--r-- 1 jovyan users   36904 Jun 25 15:34 Unix06_Bash_Bioinformatics.ipynb
-rw-r--r-- 1 jovyan users    5387 Jun 25 15:34 Unix07_Capstone_Exercise.ipynb
-rw-r--r-- 1 jovyan users    8226 Jun 25 15:34 Unix07_Capstone_Exercise_Solutions.ipynb
-rw-r--r-- 1 jovyan users   11089 Jun 25 15:34 Unix_Appendix01_Regular_Expressions.ipynb
-rw-r--r-- 1 jovyan users    6000 Jun 25 15:34 Unix_Appendix02_Review.ipynb

Fields returned by ls -l:

  • Permissions

  • Number of hardlinks

  • File owner

  • File group

  • File size

  • Modification time

  • Filename

Interpreation of permissions

-rw-r--r--

-   Regular file
rw- Owner has Read and Write permission
r-- Group has Read permission
r-- Other has Read permission

Globbing

[5]:

ls *ipynb

R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

[6]:

ls U*

Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

[7]:

ls *nix*Exercise*

Unix07_Capstone_Exercise.ipynb  Unix07_Capstone_Exercise_Solutions.ipynb

Make directories

[8]:

mkdir a
mkdir a/b
mkdir a/b/c

[9]:

ls

a
data
figs
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

[10]:

ls -R

.:
a
data
figs
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

./a:
b

./a/b:
c

./a/b/c:

./data:
gene_counts_raw.txt  gene_counts.txt

./figs:
box.png  fig1.png  fig2.png  fig3.png  fig4.png  fig5.png  g3.pdf  lm.png

./seqs:
CM000046.1.fa  CM000047.1.fa

Removing empty directories

[11]:

rmdir a/b/c
rmdir a/b
rmdir a

[12]:

ls

data
figs
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

Making nested directories in one step

[13]:

mkdir -p a/b/c a/b/d a/b/e

Create empty files

[14]:

touch a/b/c/foo.txt a/b/d/bar.txt a/b/e/baz.txt

[15]:

ls -R

.:
a
data
figs
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

./a:
b

./a/b:
c  d  e

./a/b/c:
foo.txt

./a/b/d:
bar.txt

./a/b/e:
baz.txt

./data:
gene_counts_raw.txt  gene_counts.txt

./figs:
box.png  fig1.png  fig2.png  fig3.png  fig4.png  fig5.png  g3.pdf  lm.png

./seqs:
CM000046.1.fa  CM000047.1.fa

Copying files

[16]:

cp a/b/c/foo.txt foo_copy1.txt
cp a/b/c/foo.txt a/foo_copy2.txt
cp a/b/c/foo.txt a/b/foo_copy3.txt

[17]:

ls -R

.:
a
data
figs
foo_copy1.txt
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

./a:
b  foo_copy2.txt

./a/b:
c  d  e  foo_copy3.txt

./a/b/c:
foo.txt

./a/b/d:
bar.txt

./a/b/e:
baz.txt

./data:
gene_counts_raw.txt  gene_counts.txt

./figs:
box.png  fig1.png  fig2.png  fig3.png  fig4.png  fig5.png  g3.pdf  lm.png

./seqs:
CM000046.1.fa  CM000047.1.fa

Moving files

[18]:

mv a/b/c/foo.txt a/b/c/oof.txt

[19]:

ls a/b/c

oof.txt

[20]:

mv a/b/c/oof.txt oof.txt

[21]:

ls a/b/c

[22]:

ls

a
data
figs
foo_copy1.txt
oof.txt
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

Move back

[27]:

pwd

/home/jovyan/work/Duke_HTS2019/cliburn/a/b

[28]:

cd ..

[29]:

pwd

/home/jovyan/work/Duke_HTS2019/cliburn/a

[30]:

cd ..

[31]:

pwd

/home/jovyan/work/Duke_HTS2019/cliburn

[32]:

cd a/b/c

[33]:

pwd

/home/jovyan/work/Duke_HTS2019/cliburn/a/b/c

[34]:

cd ../../../

[35]:

pwd

/home/jovyan/work/Duke_HTS2019/cliburn

Go home

[36]:

cd ~

[37]:

pwd

/home/jovyan

Go last position

[38]:

cd -

/home/jovyan/work/Duke_HTS2019/cliburn

Quick and dangerous recursive deletion

[39]:

rm -r a

[40]:

ls

data
figs
foo_copy1.txt
oof.txt
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

[41]:

rm *txt

[42]:

ls

data
figs
R00_Review_Basics.ipynb
R00_Review_Basics_Scratch.ipynb
R01_Data_Manipulation.ipynb
R01_Data_Manipulation_Scratch.ipynb
R01_Data_Manipulation_Solutions.ipynb
R01_Manipulating_Data_In_R.ipynb
R02_Tidying_Data_In_R.ipynb
R02_Tidying_Data.ipynb
R02_Tidying_Data_Solutions.ipynb
R03_FileIO.ipynb
R04_Unsupervised_Learning.ipynb
R04_Unsupervised_Learning_Scratch.ipynb
R05_Unsupervised_Learning_More_Examples.ipynb
R06_Graphics_Overview.ipynb
R07_Graphics_Base.ipynb
R08_Graphics_ggplot2.ipynb
R09_Graphics_Exercise.ipynb
R09_Graphics_Exercise_Solutions.ipynb
seqs
Unix01_File_And_Directory.ipynb
Unix01_File_And_Directory_Solutions.ipynb
Unix02_FileIO.ipynb
Unix02_FileIO_Solutions.ipynb
Unix03_File_Storage.ipynb
Unix03_File_Storage_Solutions.ipynb
Unix04_Text_Manipulation.ipynb
Unix04_Text_Manipulation_Solutinos.ipynb
Unix05_Variables.ipynb
Unix05_Variables_Solutions.ipynb
Unix06_Bash_Bioinformatics.ipynb
Unix07_Capstone_Exercise.ipynb
Unix07_Capstone_Exercise_Solutions.ipynb
Unix_Appendix01_Regular_Expressions.ipynb
Unix_Appendix02_Review.ipynb

Exercises

  1. Create the following structure including empty files using mkdir and touch commands.

crytococcus
    data
        fake1.fq
        fake2.fq
    notebooks
        my_analysis.R
        your_analysis.R
        fake3.fq
    results
        table1.csv
        table2.csv
        fig1.png
        fig2.png

[43]:

rm -rf crytococcus

[44]:

mkdir cryptococcus
cd cryptococcus
mkdir data noteboooks results
cd data
touch fake1.fq fake2.fg
cd ../noteboooks
touch my_analysis.R your_analysis.R fake3.fq
cd ../results
touch table1.csv table2.csv fig1.png fig2.png
cd ../..
ls -R cryptococcus

cryptococcus:
data  noteboooks  results

cryptococcus/data:
fake1.fq  fake2.fg

cryptococcus/noteboooks:
fake3.fq  my_analysis.R  your_analysis.R

cryptococcus/results:
fig1.png  fig2.png  table1.csv  table2.csv

  1. Navigate into the folder cryptococcus/results and find the size of fig1.png. Next make a copy of table2.csv with name table3.csv. Finally, navigate back to the same directory where this notebook is found.

[45]:

cd cryptococcus/results
ls -lh fig1.png
cd -

-rw-r--r-- 1 jovyan users 0 Jun 26 09:14 fig1.png
/home/jovyan/work/Duke_HTS2019/cliburn

  1. Move th file fake3.fq from the notebooks to the data directory.

[46]:

mv cryptococcus/noteboooks/fake3.fq cryptococcus/data

  1. List all files recursively that have the extension .R

[47]:

ls -R | grep "\.R$"

my_analysis.R
your_analysis.R

Find is a useful command that I did not have time to cover in the lecture.

[48]:

find . -name "*.R"

./cryptococcus/noteboooks/my_analysis.R
./cryptococcus/noteboooks/your_analysis.R

  1. Delete the results directory and all files in it (non-recursively).

[49]:

rm cryptococcus/results/*
rmdir cryptococcus/results

  1. Delete the cryptococcus directory recursively.

[50]:

rm -r cryptococcus

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