Is there a easier way to edit these lines

Question

I have these lines in my text files appearing

>SCRT2_DBD_NNGCAACAGGTGN
0.455331585111  0.0458438972816 0.145508011584  0.353316506023
0.173692317806  0.0247846149283 0.759302422526  0.0422206447403
1.16863332073e-07       0.940983666713  1.16863332073e-07       0.0590160995601
0.00506737765087        7.91765386614e-08       0.988123281671  0.00680926150142
0.0623177863824 0.93243216705   0.000777853090471       0.00447219347766
0.00453077729507        0.995469025719  9.8493017436e-08        9.8493017436e-08
0.507583592195  0.453364643178  0.0180440139317 0.0210077506946
>SNAI2_DBD_NRCAGGTGN
0.455331585111  0.0458438972816 0.145508011584  0.353316506023
0.173692317806  0.0247846149283 0.759302422526  0.0422206447403
>SP1_DBD_GCCMCGCCCMC
0.455331585111  0.0458438972816 0.145508011584  0.353316506023
0.173692317806  0.0247846149283 0.759302422526  0.0422206447403
1.16863332073e-07       0.940983666713  1.16863332073e-07       0.0590160995601
0.00506737765087        7.91765386614e-08       0.988123281671  0.00680926150142
0.0623177863824 0.93243216705   0.000777853090471       0.00447219347766
0.00453077729507        0.995469025719  9.8493017436e-08        9.8493017436e-08
0.507583592195  0.453364643178  0.0180440139317 0.0210077506946

And I want to get this:

>M_SCRT2
0.455331585111  0.0458438972816 0.145508011584  0.353316506023
0.173692317806  0.0247846149283 0.759302422526  0.0422206447403
1.16863332073e-07       0.940983666713  1.16863332073e-07       0.0590160995601
0.00506737765087        7.91765386614e-08       0.988123281671  0.00680926150142
0.0623177863824 0.93243216705   0.000777853090471       0.00447219347766
0.00453077729507        0.995469025719  9.8493017436e-08        9.8493017436e-08
0.507583592195  0.453364643178  0.0180440139317 0.0210077506946
>M_SNAI2
0.455331585111  0.0458438972816 0.145508011584  0.353316506023
0.173692317806  0.0247846149283 0.759302422526  0.0422206447403
>M_SP1
0.455331585111  0.0458438972816 0.145508011584  0.353316506023
0.173692317806  0.0247846149283 0.759302422526  0.0422206447403
1.16863332073e-07       0.940983666713  1.16863332073e-07       0.0590160995601
0.00506737765087        7.91765386614e-08       0.988123281671  0.00680926150142
0.0623177863824 0.93243216705   0.000777853090471       0.00447219347766
0.00453077729507        0.995469025719  9.8493017436e-08        9.8493017436e-08
0.507583592195  0.453364643178  0.0180440139317 0.0210077506946

I don't want to do it manually, as these are too many.

Please help with aone liner in awk or perl.

Here's a one-liner that might help: [`perldoc perlfaq5`](https://metacpan.org/pod/perlfaq5#How-do-I-change-delete-or-insert-a-line-in-a-file-or-append-to-the-beginning-of-a-file) — ThisSuitIsBlackNot, Sep 09 '14 at 16:57

jaypal singh · Answer 1 · 2014-09-09T17:13:06.960

3

Using awk:

$ awk -F"[>_]" '/^>/{ print ">M_" $2; next }1' file
>M_SCRT2
>M_SNAI2
>M_SP1
>M_SP3

Using perl:

$ perl -F"[>_]" -lane 'print /^>/ ? ">M_$F[1]" : $_' file
>M_SCRT2
>M_SNAI2
>M_SP1
>M_SP3

edited Sep 09 '14 at 17:13

answered Sep 09 '14 at 16:57

jaypal singh

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score 2 · Answer 2 · answered Sep 09 '14 at 17:04

2

Alternatives:

perl -pe 's/>(.*?)_.*/>M_$1/'
perl -pe 's/_.*//;s/>/>M_/'

or another sed

sed 's/_.*//;s/>/>M_/'

answered Sep 09 '14 at 17:04

clt60

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score 1 · Accepted Answer · answered Sep 09 '14 at 16:56

1

You could try the below sed command,

sed 's/^>\([^_]*\).*$/>M_\1/' file

Example:

$ sed 's/^>\([^_]*\).*$/>M_\1/' file
>M_SCRT2
>M_SNAI2
>M_SP1
>M_SP3

answered Sep 09 '14 at 16:56

Avinash Raj

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Hi Avinash, Thing is these lines appear randomly in the text file and are not one after the other. So please check the edited sample file – Angelo Sep 09 '14 at 17:00
sure, where is the sample? – Avinash Raj Sep 09 '14 at 17:01
@Angelo it would do the replacement only on the lines which starts with `>`. So the above command would for the updated sample. – Avinash Raj Sep 09 '14 at 17:04
Yeah, I see, I don't know why. But on my original data it is not working. I will try to fix it myself. Many Thanks. – Angelo Sep 09 '14 at 17:07
1

@Angelo to save the changes made to that file, you need to add inline edit parameter `-i` in the sed command, `sed -i 's/^>$[^_]*$.*$/>M_\1/' file` – Avinash Raj Sep 09 '14 at 17:08

Is there a easier way to edit these lines

3 Answers3