Help required with a script or file filter

[Nick D'Angelo]

All,

I have an output file that I need to re-format. Unfortunately, one of our tools - which can not be re-written or modified, outputs a file in this format.

CACAATGAGAAATACCTGGTGGTGCTCAGCTCA
CTCAGATTGTTCCACATATTCTAGAATAAATAA
ACGAAAGTCTAAAGTACTAAGTTTAGGCAATAC
TCTCTCTCAAGGGCTTCAGCAGGCCCCCAACCT
TACTCAAAGTATAGCAGGATAGTATATTTCAAA
and so on.

However, we want to remove the formatting or the right carriage return at the end of each line so that the output would look like this:

CACAATGAGAAATACCTGGTGGTGCTCAGCTCACTCAGATTGTTCCACATATTCTAGAATAAATAAACGAAAGTCTAAAGTACTAAGTTTAGGCAATACTCTCTCTCAAGGGCTTCAGCAGGCCCCCAACCTTACTCAAAGTATAGCAGGATAGTATATTTCAAA

Any ideas/suggestions?

This is running on Redhat 9.0.

[Jeroen Peereboom · Accepted solution]

awk 'printf "%s", $0}' filename > newfile

JP

[Stuart Browne]

Or a simpler:

tr -d "\n" < file > newfile

[Hein van den Heuvel]

And using perl....

perl -pe 'chop' < file > newfile

-p = implicit read loop and print $_ at end
-e = immediate command line
'chop' = the entire program :-). Takes last character from line which is the \n

Hein.

[KapilRaj]

cat file |tr "\n" " " # This will leave a space between them if u do not need that

cat file |tr "\n" " " |sed "s/\ //g"

Regds,

Kaps