Script to replace space with underscore using CLI

[Dagga]

Hi,

I was hoping I could help with 2 scripts to perform similiar functions.

I have a fasta file that is a combination of all the genome sequences from a specific phylum. I was hoping I could get a script that would replace every space with an underscore.

For example:

>Contig 1 Species name strain 1

>Contig 2 Species name strain 2

Will be replaces with

>Contig_1_species_name_strain_1

>Contig_2_species_name_strain_2

-------

Secondly, I was hoping for a script with the same function but will do this for filenames. I have each genome in a seperate fasta file and would like to change the file names to have underscores instead of spaces in the file name.

Thanks!

[TiborNagy]

1. It is just a command:
sed 's/ /_/g' input.fa >underscore.fa

2. The script:
#!/bin/bash
mv "$1" `echo $1 | sed 's/ /_/g'`

The $1 is a special variable for the first argument and ` open a subshell.