Question

I have a data file that I need to use an input for a program, but I need to tweak the formatting a little. Using this method: Extracting specific data from a file and writing it to another file I generated a file that looks like this:

PITG_00002  2   397
PITG_00004  1   1275
PITG_00004  1397    1969
PITG_00005  200 1111
PITG_00005  1281    1646
PITG_00006  1   816
PITG_00009  2398    3276
PITG_00009  1536    1952
PITG_00010  1   537

I need to distinguish between data that comes from the same sequence (first column) and data that comes from different sequences, by adding a blank line in between sequences that are unique, so that it looks like:

PITG_00002  2   397

PITG_00004  1   1275
PITG_00004  1397    1969

PITG_00005  200 1111
PITG_00005  1281    1646

PITG_00006  1   816

PITG_00009  2398    3276
PITG_00009  1536    1952

PITG_00010  1   537

I tagged this with the program/coding options available to me. Any help you could give is much appreciated, thanks!

Answer 1

perl -pae 'print $/ if (defined $x && $x ne $F[0]); $x = $F[0];' input.txt

This will check the first field $F[0] against the previous field, stored in $x. If they are not the same, a newline is printed.

Explanations:

• -p read file and print each line
• -a autosplit lines on whitespace into @F array
• $/ is your input record separator, default is newline.