Dividing A Protein Sequence Into Equal Parts

Question

[Nitish Mishra]

Dear All, I would be happy if anyone can suggest me command (Sed or AWK one line command) to divide each line of file in equal number of part. For example divide each line in 4 part.

Input:

ATGCATHLMNPHLNTPLML

Output:

ATGCA THLMN PHLNT PLML

Answer 1

[JC]

echo ATGCATHLMNPHLNTPLML | perl -plane '$s = int((length $_) / 4) + 1; s/(.{$s})/$1 /g;'
ATGCA THLMN PHLNT PLML

[Nitish Mishra]

When I am giving 38 character as input it gives 4 part; 3 part with 10 charter and last with 8. While I am expecting 2 part with 10 characters and last 2 with 9 character

Input: TGCATHLMNPHLNTPLMLATGCATHLMNPHLNTPLML

Output: ATGCATHLMN PHLNTPLMLA TGCATHLMNP HLNTPLML 10 Char 10 char 10 char 8 char

[Zev.Kronenberg]

try my unpack below...

Answer 2

[Zev.Kronenberg]

More than one way to skin a cat in perl :-)

echo ATGCATHLMNPHLNTPLML | perl -lane '$lag = "a4" x((length $_)/4); @seqs = unpack $lag, $_; print join " ", @seqs'

Your second example works fine with my code.

input TGCATHLMNPHLNTPLMLATGCATHLMNPHLNTPLML

output TGCA THLM NPHL NTPL MLAT GCAT HLMN PHLN TPLM

Answer 3

[Nitish Mishra]

When I am giving 38 character as input it gives 4 part; 3 part with 10 charter and last with 8. While I am expecting 2 part with 10 characters and last 2 with 9 character

Input: TGCATHLMNPHLNTPLMLATGCATHLMNPHLNTPLML

Output: ATGCATHLMN PHLNTPLMLA TGCATHLMNP HLNTPLML 10 Char 10 char 10 char 8 char

[Neilfws]

Please do not post new queries as answers; use the comments area below answers from others. Also, what you state you want is different to what you then illustrate by example. Please be precise.

[miquelduranfrigola]

Why do you want to do this? Could you please better state what are your preferences? It sounds like: "I want to break a sequence into 4 parts, not necessarily of equal length, being the shortest part the longest possible", is this right?