protein text format convert!

Question

[fufuyou]

Hi everyone,

I have some protein sequences with carriage return every line. But my program need one protein name and sequence.

Could you help me replace these carriage return?

Thanks,
Fuyou

[h.mon]

How exactly the formats (from/to)? Why don't you post small examples?

Answer 1

[13en]

If I'm understanding you correctly, and you have protein sequences like this:

>prtn1
DTENKRK
KDFLTSE
NSLPRIS

and you want

>prtn1
DTENKRKKDFLTSENSLPRISS

you could use something like this

awk 'BEGIN {ORS=""}{if ($1 ~ /^>/) print "\n"$1"\n"; else print}END{print "\n"}' <protein file>

ORS="" removes the end of line when awk prints, so the protein sequence is concatenated into one line. Checking for a line starting with ">" means the ID can be printed on its own line, by including "\n" newline characters. This can handle multiple sequences, but ends up starting with a blank line, so if your file only has one sequence you might want to replace "\n"$1"\n" with $1"\n".