Modifying a line

Shell Programming and Scripting
1

Hi,

I am having trouble modifying this line. It is because there is a space that I dont know how to deal with.

So the file looks like this

>YM4911-Contig4 [name=joe]
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>YM4915-Contig5 [name=bob]
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM

There are two spaces between contig# and [name=x] in some files and a single space in other files. How would write a command to deal with both?

I want to modify the file so it looks like this.

>Contig4
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>Contig5
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM

This is the format that I am trying to get..

thanks

2

this will do i guess..

sed 's/\(.*\)\(Contig[0-9]\)\(.*\)/\2/g' filename
3

the output is like this:

Contig4
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Contig5
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM

How do I maintain the > so it will look like this:

>Contig4
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>Contig5
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM

4

make small change..

sed 's/\(>\)\(.*\)\(Contig[0-9]\)\(.*\)/\1\3/g' filename
5

I have another question.

the contig goes pass 9... so it will go up to like 5000

How does the sed line deal with that?

thanks

6

hmmmm..

sed 's/\(>\)\(.*\)\(Contig[0-9]*[0-9]\)\(.*\)/\1\3/g' filename
7

With awk:

awk -F" |-" '/Contig/{print ">" $2;next}1' file