Class 3: Folders and Files

Computing for Molecular Biology 1

Andrés Aravena

19 October 2020

Structure of secondary memory

The disks store a huge amount of data

To organize it we use files

To organize the files we use folders
also called directories

Folders, also called Directories

You probably know about computer folders

They are an example of hierarchical structure

Key idea:

you work in the current directory
you can change your current directory
be aware of what is your current directory

Files

Like the main memory, a file is just a list of bytes

The meaning of the file depends on the context

Usually, the name of the file suggests a context

For example, an MP3 file is probably audio

File attributes

Besides the data itself, files have metadata

That is, data about the data. For example

Files have a name
Files have a modification date, maybe other dates too
Files have a size

You should learn how to read them

File names

The names of the files are “words”:

a series of letters, numbers and some symbols
Technically, a filename is a string or list of characters

Maximum length of a filename is 250 characters

File names

You can use

English letters (A-Z, a-z),
numbers (0-9),
some symbols: ., -, and _

You cannot use any of these symbols:
/, :, +, |, <, *, >, " and '

You can use (space) and non-english letters (like ǧ or ñ)
but I recommend not to use them, because they may cause problems

File names

In some systems small caps and BIG CAPS are not equivalent

For example HOMEWORK.txt and homework.txt are different

Be careful. Be systematic and coherent:

Use always the same name
Easy way: use only lower case

File extensions

If the filename includes ., the text after it is called extension

In Microsoft Windows® extensions are usually 3 letters

For example

File extensions

It is a suggestion on how to interpret the file

Images: JPG, PNG, GIF, TIFF
Movies: AVI, MP4, MOV
Audio: WAV, MP3
Documents: DOC, DOCX, PDF
Genomic data: GBK, FNA, FAA
Programs: EXE, APP

Kinds of file

It is useful to separate computer files in two groups:

Text Files: each byte is a character, we can read it
Binary Files: bytes are grouped in binary numbers, representing images, sounds, etc.

Content of a binary file

binary file

Content of a text file

text file

Binary files are only for computers

It is very hard to understand a binary file without a computer
It can only be read by the program that made it
Most of these programs are private
If the company goes out of business, you lose your data
New versions of the program may not read the old files

Text files are for humans and computers

Binary files are hard to read
- unless you have the correct program
Text files can be read by humans
- Each byte is a letter
Text files can be read by computers
- Data must be recyclable
- The output of one program may be the input of another program

Text files are for ever

Free

nothing to pay
you can do whatever you want

Never get obsolete

We can still read the programs that controlled the Apollo Lunar Module in 1969
“Archiving and referencing the Apollo source code”

Word® files are not text files

(doc or docx)

You shall not use Microsoft Word® to handle data

Text Files

are universal
are easy to read and write from a program
do not have any style like bold or italic
are like books without figures

The natural way to represent a text document is to encode each letter with a single byte

There is a basic standard for English, called ASCII

ASCII code

Each letter is coded by a number

	30	40	50	60	70	80	90	100	110	120
0		(	2	<	F	P	Z	d	n	x
1		)	3	=	G	Q	[	e	o	y
2			4	>	H	R	\	f	p	z
3	!	+	5	?	I	S	]	g	q	{
4	"	,	6	@	J	T	^	h	r	\|
5	#	-	7	A	K	U		i	s	}
6	$	.	8	B	L	V	`	j	t	~
7	%	/	9	C	M	W	a	k	u
8	&	0	:	D	N	X	b	l	v
9	´	1	;	E	O	Y	c	m	w

ASCII code

Each number from 0 to 127 is either a symbol or a special signal

New Line
End of Message
Tab
Space
Backspace

Non-English languages use numbers between 128 and 255 for symbols like “Ç”, “Ö”, “É”, “Ñ”

To learn more

https://en.wikipedia.org/wiki/Binary_file https://en.wikipedia.org/wiki/Text_file https://en.wikipedia.org/wiki/Directory_(computing) https://en.wikipedia.org/wiki/List_of_file_formats

Questions?

Homework: Install R 4.0 in your computer

For this course we will use the new version of R and Rstudio. These two tools work together. Install R first, then install Rstudio.

These videos may help you

Now

Fill the survey at the course homepage

Visit dry-lab.org/blog/2020/cmb1 and fill the survey

	30	40	50	60	70	80	90	100	110	120
0		(	2	<	F	P	Z	d	n	x
1		)	3	=	G	Q	[	e	o	y
2			4	>	H	R	\	f	p	z
3	!	+	5	?	I	S	]	g	q	{
4	"	,	6	@	J	T	^	h	r	\|
5	#	-	7	A	K	U		i	s	}
6	$	.	8	B	L	V	`	j	t	~
7	%	/	9	C	M	W	a	k	u
8	&	0	:	D	N	X	b	l	v
9	´	1	;	E	O	Y	c	m	w

	30	40	50	60	70	80	90	100	110	120
0		(	2	<	F	P	Z	d	n	x
1		)	3	=	G	Q	[	e	o	y
2			4	>	H	R	\	f	p	z
3	!	+	5	?	I	S	]	g	q	{
4	"	,	6	@	J	T	^	h	r	\|
5	#	-	7	A	K	U		i	s	}
6	$	.	8	B	L	V	`	j	t	~
7	%	/	9	C	M	W	a	k	u
8	&	0	:	D	N	X	b	l	v
9	´	1	;	E	O	Y	c	m	w

	30	40	50	60	70	80	90	100	110	120
0		(	2	<	F	P	Z	d	n	x
1		)	3	=	G	Q	[	e	o	y
2			4	>	H	R	\	f	p	z
3	!	+	5	?	I	S	]	g	q	{
4	"	,	6	@	J	T	^	h	r	\|
5	#	-	7	A	K	U		i	s	}
6	$	.	8	B	L	V	`	j	t	~
7	%	/	9	C	M	W	a	k	u
8	&	0	:	D	N	X	b	l	v
9	´	1	;	E	O	Y	c	m	w