sed find an replace help

[M. Olalla Lorenzo-Carballa]

Dear all

I do have a text file with several lines, each of them with the following structure:

Cluster-28302_1_TRINITY_DN11551_c0_g1_i2

Were I need to replace "Cluster-28302_1_TRINITY" for "Cluster-28302-1_TRINITY"

I have been trying to used find and replace with sed but up to know I am not able to get it right. I did the following:

cat test-sed| sed -r 's/_[0-9][0-9]*_TRINITY/.[0-9][0-9]*_TRINITY/'g

and this is what I do get:

Cluster-11746_1    Cluster-11746.[0-9][0-9]*_TRINITY_DN20997_c0_g2_i5
Cluster-11746_0    Cluster-11746.[0-9][0-9]*_TRINITY_DN20997_c0_g1_i1
Cluster-30178_1    Cluster-30178.[0-9][0-9]*_TRINITY_DN20362_c5_g1_i2
Cluster-28828_0    Cluster-28828.[0-9][0-9]*_TRINITY_DN20970_c2_g1_i1
Cluster-22499_0    Cluster-22499.[0-9][0-9]*_TRINITY_DN18016_c0_g2_i1
Cluster-22499_0    Cluster-22499.[0-9][0-9]*_TRINITY_DN18016_c0_g1_i2
Cluster-22499_0    Cluster-22499.[0-9][0-9]*_TRINITY_DN18016_c0_g1_i1
Cluster-8219_1    Cluster-8219.[0-9][0-9]*_TRINITY_DN17010_c1_g1_i3

I would be thankful if anyone could help me to find the right command to do it... I am sure it is easy and simple :S

Thanks a lot in advance

Olalla

[Keith Bradnam]

cat test-sed | sed 's/_TRINITY.*/-TRINITY/'

[Melissa A. Wilson Sayres]

sed -e 's/_/-/' test-sed | sed -e 's/-TRINITY/_TRINITY/' 

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Melissa A. Wilson Sayres, PhD

Assistant Professor of Genomics, Evolution, and Bioinformatics

The Biodesign Institute

School of Life Sciences

Arizona State University

[Pedro jose Martinez]

Maybe that:

cat test-sed | sed -e 's/\_/-/' 

Cluster-11746-1_TRINITY_DN20997_c0_g2_i5

Cluster-11746-0_TRINITY_DN20997_c0_g1_i1

Cluster-30178-1_TRINITY_DN20362_c5_g1_i2

Cluster-28828-0_TRINITY_DN20970_c2_g1_i1

Cheers,

PJ

[Pedro jose Martinez]

better:

cat test-sed | sed -e 's/\_/-/' | cut -d_ -f 1-2

Cheers,

PJ