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View and Search Text and Directories

View and Search Text and Directories

Goal: Use various commands to view, inspect and search a text file.

Exercise: Setting Up

Question:

  • There is a folder called intro_to_linux within the /project/<project-name>/ folder.

  • How would you copy this folder into your home folder?

  • Before moving on, please make sure you get this copied over correctly.

  • All further exercises assume you will be working within this folder, within the home folder

  • As you work through exercises take note of the []$ cd ~/intro_to_linux - remember the tilda character ~ is a shortcut for the home folder.

Setting Up: Answer(s)

Answer: There are a number of ways…

Method 01: Move into your home folder and copy into this location.

The . marks the current working directory.

[]$ cd [~]$ cp -r /project/<project-name>/intro_to_linux/ . cp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied [~]$ ls Desktop Documents Downloads intro_to_linux

Method 02: Move into the /project/<project-name>/ folder and copy from there, into your home.
Remember, the ~ is short for your home folder.

[~]$ cd /project/<project-name>/ [<project-name>]$ cp -r intro_to_linux/ ~ cp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied [<project-name>]$ ls ~ Desktop Documents Downloads intro_to_linux

In both cases you do not have permissions to copy workshop_me.txt - this is intentional and a good remind to check the permissions/ownerships of files.

Question: What do you notice about the permissions of this file?

# -rw------- 1 <arcc-username> <project-name> 23 Oct 5 07:20 workshop_me.txt

Only the owner of this file (<arcc-username>) has permission to read/write, and thus copy this file.

Any other user can not copy this file, and thus it will not be copied as part of everything else.

View the content of files

Command

Description

cat

Usage: cat [OPTION]... [FILE]... Concatenate FILE(s) to standard output.  -n, --number               number all output lines

more

more [options] <file>... A file perusal filter for CRT viewing. more  is a filter for paging through text one screenful at a time.

head

Usage: head [OPTION]... [FILE]... Print the first 10 lines of each FILE to standard output.  -n, --lines=[-]NUM       print the first NUM lines instead of the first 10;                              with the leading '-', print all but the last                              NUM lines of each file

View the content of files

Command

Description

tail

Usage: tail [OPTION]... [FILE]... Print the last 10 lines of each FILE to standard output.  -f, --follow[={name|descriptor}]                            output appended data as the file grows;                              an absent option argument means 'descriptor’  -n, --lines=[+]NUM       output the last NUM lines, instead of the last 10;                              or use -n +NUM to output starting with line NUM

Exercises: View Files: Give it a go.

Question: Within the intro_to_linux folder, how can we view the contents of the software.csv file?

  1. How can we view the entire file?

  2. How can we view the start of the file?

  3. How can we view the end of the file?

Answers

Within the intro_to_linux folder, how can we view the contents of the software.csv file?

1. How can we view the entire file?

[]$ cd ~/intro_to_linux/ [intro_to_linux]$ cat software.csv [intro_to_linux]$ cat -n software.csv [intro_to_linux]$ more software.csv # Press spacebar to scroll through. # Press ‘q’ to quit at any time.

2. How can we view the start of the file?

[intro_to_linux]$ head software.csv [intro_to_linux]$ head –n 5 software.csv

3. How can we view the end of the file?

[intro_to_linux]$ tail software.csv [intro_to_linux]$ tail –n 5 software.csv

Search for a string within a text file (grep) 

Command

Description

grep

Usage: grep [OPTION]... PATTERN [FILE]... Search for PATTERN in each FILE. Example: grep -i 'hello world' menu.h main.c ... -i, --ignore-case ignore case distinctions ... -n, --line-number print line number with output lines ... -r, --recursive like --directories=recurse ... # grep is case-sensitive

Examples: Search a file

Remember, Linux in general, and grep are case-sensitive.

Search for the capitalized NVIDIA text.

[intro_to_linux]$ grep nvidia software.csv [intro_to_linux]$ # Remember: grep is case-sensitive [intro_to_linux]$ grep NVIDIA software.csv libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep... libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...

The above identified and returned two locations where NVIDIA was found.

But this would not pick up the text Nvidia.

Modify the command-line to ignore-case using the -i option.

[intro_to_linux]$ grep -i NVidia software.csv compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"... libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep... libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...

Modify the command-line to display the the line numbers within the file using the -n option.

[intro_to_linux]$ grep -n -i NVidia software.csv 145:compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"... 152:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep... 166:libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...

Examples: Search folders and files

Use the wildcard * to search all files within the folder.

[intro_to_linux]$ cd clusters/ [clusters]$ grep -i nvidia * beartooth.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td> teton.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td> [clusters]$ cd ..

Remember: case-sensitivity:

[intro_to_linux]$ grep -i nvidia * grep: clusters: Is a directory software.csv:compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"... software.csv:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep... software.csv:libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...

Modify the command-line, using the -r option, to recursively search through folders within this folder.

[intro_to_linux]$ grep -r -i nvidia * clusters/teton.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td> clusters/beartooth.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td> software.csv:compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"... software.csv:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep... software.csv:libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...

Exercises: Search Files

We will be using the software.csv file:

Lets take a quick look at it using head to view the first few lines. How is this structured? What columns do we have?

# The software.csv file takes the form: [intro_to_linux]$ head software.csv Type,Name,Module,Cluster,Description application,Alphafold,alphafold,"beartooth,teton",AlphaFold... application,Astral,astral,wildiris,ASTRAL is a tool... application,Augustus,augustus,beartooth,AUGUSTUS is a program... application,Avizo,avizo,loren-pre202308,Avizo is a general-purpose... application,ANGSD,angsd,"beartooth,teton",ANGSD: is a software... application,ANSYS,ansys,teton,"ANSYS is a general-purpose software...

Questions:

  1. Which named applications are related to the words bayes?

  2. Which files contain reference to IPA?

Answers

Question 01: Which named applications are related to the words “bayes”?

We have a csv file, with comma separated columns, the second column represents the name of the application.

This assumes we want to find all instances of “bayes” regardless of case.

[intro_to_linux]$ grep -i bayes software.csv application,Bayescan,bayescan,beartooth,"BayeScan aims... application,Beast1,beast1,wildiris,BEAST is a cross-platform program for Bayesian... application,Beast2,beast2,beartooth,"BEAST 2 is a cross-platform program for Bayesian... application,Freebayes,freebayes,beartooth,"freebayes is a Bayesian genetic... application,Jags,jags,"beartooth,teton",Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical... application,RevBayes,revbayes,wildiris,Bayesian phylogenetic... application,ROHan,rohan,teton,"ROHan is a Bayesian framework... application,SourceTracker2,sourcetracker2,"beartooth,teton","SourceTracker, a Bayesian approach...

Which of the returned lines represent an application with bayes within it’s name column?

[intro_to_linux]$ grep -i bayes software.csv application,Bayescan,bayescan,beartooth,"BayeScan aims... application,Freebayes,freebayes,beartooth,"freebayes is a Bayesian genetic... application,RevBayes,revbayes,wildiris,Bayesian phylogenetic...

The other returned lines are “lines that contain the word bayes within it” - so not strictly what we are looking for.

Question 02: Which files contain reference to IPA?

In this case we want to explicitly search for IPA (all upper-case) and recursively search through all folders.

[intro_to_linux]$ grep -r IPA * clusters/beartooth.html: .../pages/1893597185/IPA">IPA</a></td> software.csv:application,IPA,ipa,beartooth,Improved Phased Assembler (IPA) is...

 

 

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