Hcfyk

I have a file with ~ 3 million rows, here is the first few lines of my file:

head out.txt

    NA

    NA

    NA

    NA

    NA

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753,gene85754

    gene85752,gene85753,gene85754

    gene85752,gene85753,gene85754

    gene85752,gene85753,gene85754

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752,gene85753

    gene85752

    gene85752

For those rows that are separated by ",", I want to keep everything after the first comma and before the second comma.
This is my desired output:

outgood.txt

NA

NA

NA

NA

NA

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85752

gene85752

Since cut prints non-delimited lines by default the following works

cut -f2 -d, file

awk -F, 'NF > 1 { $1 = $2 } { print $1 }' file

This uses awk to parse the file as lines consisting of comma-delimited fields.

The code detects when there is more than a single field on a line, and when there is, the first field is replaced by the second field. The first field, either unmodified or modified by the conditional code, is then printed.

awk -F, 'NF == 1 {print $1}

         NF > 1 { print $2}' filename

This will print just the first string if there is no comma, second string if there is one or more comma.

You can do this with Perl as follows.

Command-line:

$ perl -F, -pale '$_ = $F[1] // $_' out.txt

Explanation:

• 
  -p will read records line-by-line AND autoprint before going in to read the next or eof.


• 
  -l makes IRS = ORS = "n"
  


• 
  -F, makes FS a comma.


• 
  -a splits each record $_ on the field separator, in our case a comma, and goes ahead and stores the fields so generated in the array @F, which is zero-indexed.


• 
  -e implies, what follows it is the Perl code, which shall be gets applied to each record.


• 
  $_ = $F[1] // $_ expression reads as follows: if the 2nd field $F[1] isn't defined, use the current record $_. And then the result of this expression is assigned to the current record $_.


• owing to the -p switch of perl being in use, before the new record is read in, the current record is taken to stdout.

Result:

NA

NA

NA

NA

NA

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85753

gene85752

gene85752

You may also do it with the GNU version of the sed editor as shown below:

$ sed -ne '

    s/,/n/

    s/.*n//

    s/,/n/

    P

' out.txt