Linux – how to insert new line if a line has more than 60 characters

awklinuxsedtext;

I need to turn a text file that has a single line per file name and output separated by a single space into specific blocks that have lines that are equal to 60 characters in length.

Like this:

>Directory1/file3 CTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCCCCSCBCCCCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCCCCSCBCCCCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCCCCSCBCCCCCCCCS
>Directory1/file4 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
...
...

turn into

>Directory1/file3
CTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCCCCSCBCC
CCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCC
CCSCBCCCCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTT
TCCCCCCCCSCBCCCCCCCCS
>Directory1/file4
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAA
...
...

How do I go about this?

Best Answer

Try:

$ awk '{print $1; for (i=1;i<=length($2);i=i+60) print substr($2,i,60)}' file
>Directory1/file3
CTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCCCCSCBCC
CCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCC
CCSCBCCCCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTT
TCCCCCCCCSCBCCCCCCCCS
>Directory1/file4
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAA

How it works:

print $1

This prints the first field on the line.
for (i=1;i<=length($2);i=i+60) print substr($2,i,60)

For the second field on the line, we print 60 characters at a time until we reach the end of the field.

Method #1

Since you only are interested in lines if they have more than 2 characters separated by commas you could just grep for commas:

$ grep "," sample.txt 
chr2          3323     C    T,A
chr3          5251     C    T,G
chr3          9990     G    C,T

Method #2

You could use grep's PCRE facility. This is where grep can use Perl's regular expression engine to do the matching. It's quite powerful and lets you do a lot of what you can do with Perl from grep.

loosely defined

$ grep -P "(\w,)+" sample.txt

strictly defined

$ grep -P '\w+\d\s+\d+\s+\w\s+(\w,)+' sample.txt

Method #3

Using awk. This again is taking advantage of the fact that only the lines with a comma (,) are of interest, so it just finds them and prints them:

loosely defined

$ awk '/,/{print}' sample.txt

more strictly defined

$ awk '/([[:alpha:]])+,[[:alpha:]]/{print}' sample.txt

even more strictly defined

$ awk '$4 ~ /([[:alpha:]])+,[[:alpha:]]/{print}' sample.txt

This one looks at the contents of the 4th column and checks that it's a letter followed by a comma, followed by another letter.

even more strictly defined

$ awk '$4 ~ /([GATC])+,[GATC]/{print}' sample.txt

This looks for only a G,A,T, or C followed by a comma, followed by another G,A,T or C.

Bash – How to “grep” for line length in a given range

grep -x '.\{3,10\}'

where

-x match pattern to whole line
. any symbol
{3,10} quantify from 3 to 10 times previous symbol (in the case any ones)

Best Answer

Related Solutions

sed and awk – How to Extract Line from File on Specific Condition

Method #1

Method #2

Method #3

Bash – How to “grep” for line length in a given range

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