topic Re: Help required with a script or file filter in Operating System - Linux

Help required with a script or file filter

Nick D'Angelo — Wed, 09 Jun 2004 14:41:27 GMT

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.

Re: Help required with a script or file filter

Jeroen Peereboom — Wed, 09 Jun 2004 15:25:37 GMT

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

JP

Re: Help required with a script or file filter

Stuart Browne — Wed, 09 Jun 2004 19:11:25 GMT

Or a simpler:

tr -d "\n" < file > newfile

Re: Help required with a script or file filter

Hein van den Heuvel — Wed, 09 Jun 2004 22:09:17 GMT

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.

Re: Help required with a script or file filter

KapilRaj — Wed, 09 Jun 2004 23:02:29 GMT

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