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Process alternate lines in awk/sed/perl

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# 1  
Old 07-15-2013
Process alternate lines in awk/sed/perl
hi..

i have a fasta file with the following format

Code:
>sequence1
CCGGTTTTCGATTTGGTTTGACT
>sequence2
AAAGTGCCGCCAGGTTTTGAGTGT
>sequence3
AGTGCCGCAGAGTTTGTAGTGT

Now, i want to read alternate line and add "GGGGGGGGGGG" to end of every sequence

Desired output:

Code:
>sequence1
CCGGTTTTCGATTTGGTTTGACTGGGGGGGGGGG
>sequence2
AAAGTGCCGCCAGGTTTTGAGTGTGGGGGGGGGGG
>sequence3
AGTGCCGCAGAGTTTGTAGTGTGGGGGGGGGGG

Moderator's Comments:
Mod Comment Please use CODE tags to mark code, input, and output samples.


---------- Post updated at 11:06 PM ---------- Previous update was at 11:00 PM ----------

---------- Post updated at 11:06 PM ---------- Previous update was at 11:06 PM ----------

I was trying the following command and missed a simple flower brace and struggling. Now i figured it out and working fine.. thanks..
Code:
awk 'NR % 2 {print} !(NR % 2) {print $0"GGGGGGGGG"}' seq.fa

Last edited by Don Cragun; 07-15-2013 at 12:04 AM.. Reason: Add CODE tags
# 2  
Old 07-15-2013
Try something like:
Code:
sed '/^[^>]/s/$/GGGGGGGGGGG/' fasta.txt

# 3  
Old 07-15-2013
try..

Code:
 
printf "%s\n%sGGGGGGGGGGG\n" $(cat filename)

# 4  
Old 07-15-2013
Quote:
Originally Posted by vidyadhar85
try..

Code:
 
printf "%s\n%sGGGGGGGGGGG\n" $(cat filename)

This isn't a robust approach under any circumstance. When dealing with possibly large amounts of bioinformatics data, it's even less so.

Regards,
Alister
# 5  
Old 07-16-2013
Quote:
Originally Posted by alister
This isn't a robust approach under any circumstance. When dealing with possibly large amounts of bioinformatics data, it's even less so.

Regards,
Alister
Thanks..

I never mentioned its "THE BEST" option I wanted to show if one have small amount of date there is no need to use fancy sed/awk alays Smilie

Its upto one how he/she read/take it..

Regards,
Vidya
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