UNIX for Dummies Questions & Answers

Hello All,

this is my first post so I don't know if I am doing this right.

I would like to append entries from a series of strings (contained in a text file) consecutively at the end of specifically labeled lines in another file.

As an example:

- the file that contains the values to be added (cluster_sizes.txt):

Code:

;size=3
;size=142
;size=21

- the file these entries shall be added to at the end of each line that begins with ">" (rep_sequences.fasta):

Code:

>seq_3453 source=sludge
AGCATTAGATCCATAGACTACAG
>seq_92 source=water 
CAGGATACAGTACACAGTACAGTACA
>seq_24 source=filter
AGTGACAGTACCCCGTAGACAGTA

so the output should look like:

Code:

>seq_3453 source=sludge;size=3
AGCATTAGATCCATAGACTACAG
>seq_92 source=water;size=142
CAGGATACAGTACACAGTACAGTACA
>seq_24 source=filter;size=21
AGTGACAGTACCCCGTAGACAGTA

is this possible with awk or some similar language/ command? I have been searching on the net but don't really know how to get towards the needed information. I am a newbie to this world of text manipulation.

Any help is greatly welcome, thanks in advance!

Gus

An awk approach:

Code:

awk 'NR==FNR{A[++c]=$0;next}/^>/{$0=$0 A[++j]}1' cluster_sizes.txt rep_sequences.fasta

Try:

Code:

nawk 'NR==FNR{a[NR]=$0;next}/^>/{$0=$0""a[++i]}1' cluster_sizes.txt rep_sequences.fasta

Wow, that was incredibly fast and it works like a charm. Thank you so much! The real Yoda you certainly are.

And another answer! Thank you Bartus!

Both solutions do exactly what I was looking for, thanks a ton!

edit: I'll take this as motivation to learn this language, I had no idea it was so powerful.