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Basic Unix Commands 3: File Naming

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Command Line Tools for Genomic Data Science

Université Johns-Hopkins

4.2 (297 notes) | 13K étudiants inscrits

Cours 5 de 8 dans Science des données génomiques Spécialisation

Introduces to the commands that you need to manage and analyze directories, files, and large sets of genomic data. This is the fourth course in the Genomic Big Data Science Specialization from Johns Hopkins University.

Visualiser le programme de cours

Compétences que vous apprendrez

Bioinformatics, Samtools, Unix, Command-Line Interface

Avis

4.2 (297 notes)

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WL

Jul 07, 2016

This is perhaps one of the most clearly taught courses I have had on Coursera. Thank you for putting in time to teach us!

GY

Aug 29, 2017

Highly recommended.\n\nI suggest you take it before "Genomic Data Science with Galaxy".

À partir de la leçon

Basic Unix Commands

In this module, you will be introduced to command Line Tools for Genomic Data Science

Basic Unix Commands 1: Content Representation3:29

Basic Unix Commands 2: Files, Directories, Paths7:29

Basic Unix Commands 3: File Naming4:00

Basic Unix Commands 4: Content Creation9:28

Basic Unix Commands 5: Accessing Content I6:25

Basic Unix Commands 6: Accessing Content II4:55

Basic Unix Commands 7: Redirecting Content6:10

Basic Unix Commands 8: Querying Content15:43

Basic Unix Commands 9: Comparing Content11:18

Basic Unix Commands 10: Archiving Content13:42

Basic Unix Commands 11: Practical Exercises I13:11

Basic Unix Commands 12: Practical Exercises II9:14

Enseigné par

Liliana Florea, PhD
Assistant Professor

Transcription

In this section, we will continue to talk about content representation in Unix, and

we will look at how we can effectively name files, particularly,

when we have large numbers of files that are of a particular type.

So, if we're looking at the content of the current directory for our application,

LS would show us that we have three types of files for each of the three species.

The three species are apple, peach, and pear, and for

each of the species, we have a genome file, a genes file and a samples file.

So that's simple, right?

But now, let's imagine that we have 100 species, and

that we have 1,000 files for each one.

Well, how can we represent, or how can we least files, in that case efficiently?

We can use the so called naming patterns.

We can use wild cards.

For instance, one very popular wild card, and very useful one, is the star.

So star represents any combination of letters and numbers, so any string.

So we can very simply type now, list all the fives that are associated

with the species apple, apple.star, and that would

give us the three files that correspond to the species apple, apple.genes,

apple.genome, and apple.samples.

And we can do so with the other species as well.

Another wild card, that now stands for

just one character, is marked with a question mark.

So, for instance,

we can say ls ?pple.genome, and

this will return apple.genome.

So, as you can see, the question mark stands for

the a at the beginning of file name.

We can also represent a range of characters in square brackets.

So we can say, square brackets,

any lower case letter between A and Z, multiple times,

and this what star stands for, .genome.

So this is a representation that will give us all the files that have the extension

genome.

Apple.genome, peach.genome,

and pear.genome.

We can also do combinations.

So for instance,

we can look at all the genomes files whose name starts with the letter P.

LS p star .genome, and

that will give us peach.genome and

pear.genome.

Lastly, there's one more way of representing one more

naming pattern that I would like to show you, which is the curly brackets.

So in curly brackets, we can specify a number of options.

So we can say, ls open curly bracket pear,

peach.genome, and it will list all the files

that have either pear or peach at the beginning

of the file name, followed by .genome.

So in this case, peach.genome and pear.genome.

So this way we can represent a very large number of files that share a common naming

pattern in a very effective way.

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