Chain commands

stdin/stderr/stdout

The shell

reads the command input from the keyboard
writes the command output to the screen,
it writes errors on screen too.

File descriptors

Each process that the shell creates, works with file descriptors.

File descriptors determine where the input to the command originates and where the output and error messages are sent.

Number	Abbreviation	Definition
0	stdin	Standard command input
1	stdout	Standard command output
2	stderr	Standard command error

All commands that process file content read from the standard input and write to the standard output.

File descriptor (example)

The following example shows the standard input (bold text) and the standard output (plain text) for the cat command.

Press Control-D to exit the cat command.

$ cat (Read from stdin)

First line (Read from stdin)

First line (Write to stdout)

What's going on? (Read from stdin)

What's going on? (Write to stdout)

Control-d (Read from stdin)

The cat command takes the standard input from the keyboard and sends the standard output to the terminal window.

redirection

You can modify the default action of the standard input, standard output, and standard error within the shell by redirecting stdin, stdout, and stderr.

Redirecting Standard Input

The following syntax example shows a
command using the less than (<) character
to process a file as the standard input
instead of reading the input from the keyboard.

command < filename

exrecises:

Use command tr to transform sequence
~/DataBio/Sequences/Nucleique/qr1.fasta
from lower case into upper case.
(use man tr to get explanation about tr command)

Redirecting Standard Output

command > filename

redirect the standard output in to a file named filename

Warning

If the file in which we redirect the stdout already exist, the file will be erased.

exercise:

use squizz program to transform the sequence file ~/DataBio/Sequences/Nucleique/qr1.gb from genbank format into fasta format

The squizz command syntax:

squizz -c FASTA sequence_file

Redirecting Standard Output

Instead to erase the file, we can append the stdout at the end of the file, using >>.

exercises:

Use squizz to create a multi fasta file with the following entries:

il2_human (~/DataBio/Sequences/Proteique/il2_human.sp)
il2_mouse (~/DataBio/Sequences/Proteique/il2_mouse.sp)
il2_rabit (~/DataBio/Sequences/Proteique/il2_rabit.sp)
il2_rat (~/DataBio/Sequences/Proteique/il2_rat.sp)
il2_sheep (~/DataBio/Sequences/Proteique/il2_sheep.sp)

Redirecting Standard Error

To redirect the stderr, we have to name explicetly the file descriptor to redirect 2>.
we can use 2>> to append to a file.

quizz

how to redirect stdout and stderr in same file?

squizz -c FASTA qn1.gb > qn1.fa 2>&1
Warning

2>&1 there is no spaces between >and &1

The chain command

the pipe (|) character to redirect the stdout to the stdin of another command.

command_1 | command_2

who | wc -l
35

who is connected?
- who | cut -f 1 -d ' '| sort | uniq
is bneron is connected?
- who | grep bneron

How do I run several commands in Sequence or all at once?

several commands can be chained with a ; (semi colon).

command1;command2;command3

exercise:

transform ~/DataBio/Sequences/Nucleique/qr1.gde in fasta format
store the result in a file qr1.fa
transform fasta sequence in upper case
and store the result in QR1.FA file
all in one command line

squizz -c FASTA ~/DataBio/Sequences/Nucleique/qr1.gde > qr1.fa ; tr 'acgt' 'ACGT' < qr1.fa > QR1.FA

limitation

squizz -c FASTA qr1.gd > qr1.fa ; tr 'acgt' 'ACGT' < qr1.fa > QR1.FA

Here there is no consequences.

But if my command is more complex like squizz -c FASTA qr1.gd > qr1.fa ; blastall -p blastp -d sp -i qr1.fa

I'd like to run a step, only if the previous one finish correctly.

what does mean finish correctly?

return values / exit status

when a program finish it return value:

0 for success.
non zero for failure.

echo $? allow to know the return value of the last command.

; chain commands whatever is the return value

chain commands

command1 && command2

command2 will be executed if and only if command1 returned zero exit status.

Warning

The exit status depends how the developer implement programs. Sometimes the developer does not follow the convention. So it's not possible to chain correctly those programs.