Printing different fields from different lines

Question

I have a file as shown bellow

G1 A1 X 3 6 NA 7 NA NA NA 7 NA NA
G1 B1 X NA NA NA NA NA NA NA NA 7 6
G1 C1 X NA 1 3 4 NA NA NA NA NA NA
G2 D1 Y NA NA NA 1 NA NA NA NA NA NA
G2 E1 Y 2 NA NA NA NA NA NA NA NA NA
G2 F1 Y NA NA NA NA 0 NA NA NA NA NA
G1 G1 Y NA NA NA NA NA 8 7 NA NA NA
G2 H1 X NA NA NA NA NA NA NA NA NA NA

Now I want to print those fields which are not equivalent to NA. Again I don't want to change the 1st three column format but after that I want to print remaining fields as separated by comma, output file I want as

G1 A1 X 3, 6, 7, 7 
G1 B1 X 7, 6
G1 C1 X 1, 3, 4
G2 D1 Y 1
G2 E1 Y 2 
G2 F1 Y 0 
G1 G1 Y 8, 7 
G2 H1 X

I tried doing

sed 's/NA//g' file| sed 's/\t/ /g'| sed 's/ \+/, /g'

But it changing the format of the first three column also. Can you suggest something for this.

Thanks

Answer 1

Here us an awk

awk '{gsub(/ NA/,"");for (i=4;i<NF;i++) $i=$i","}1' file
G1 A1 X 3, 6, 7, 7
G1 B1 X 7, 6
G1 C1 X 1, 3, 4
G2 D1 Y 1
G2 E1 Y 2
G2 F1 Y 0
G1 G1 Y 8, 7
G2 H1 X

Answer 2

This is complicated enough that I would reach for perl.

perl -pe '
    chomp; s/\s+/ /g; s/ $//; s/^ //;
    my ($left, $right) = /(\S+ \S+ \S+) (.+)$/;
    $right =~ s/\bNA\b//g;
    $right =~ s/^ +//;
    $right =~ s/ +$//;
    $right =~ s/ +/, /g;
    $_ = "$left $right";
    s/ *$/\n/;
'

DTRT on your test case, someone cleverer and/or less sleepy than me might be able to golf it down a bit.

Answer 3

Here is another way using awk:

awk '{gsub(/NA/,"");$1=$1;for(i=4;i<=NF;i++)$i=(i==NF?$i:$i",")}1' file
G1 A1 X 3, 6, 7, 7
G1 B1 X 7, 6
G1 C1 X 1, 3, 4
G2 D1 Y 1
G2 E1 Y 2
G2 F1 Y 0
G1 G1 Y 8, 7
G2 H1 X

or using GNU sed:

sed -e 's/\bNA\b//g' -e 's/ \+/ /g' -e 's/ *$//' -e 's/ /, /4g' file
G1 A1 X 3, 6, 7, 7
G1 B1 X 7, 6
G1 C1 X 1, 3, 4
G2 D1 Y 1
G2 E1 Y 2
G2 F1 Y 0
G1 G1 Y 8, 7
G2 H1 X

Answer 4

sed ':a
s/\(\([^]\{1,\} \{1,\}\)\{2\}[^ ]\{1,\}\)\(.*\) NA/\1\3/
t a
' YourFile

normaly should also work with the generic class [:blank:] instead of space character (code below) but strangely failed on my system

sed ':a
s/\(\([^[:blank:]]\{1,\}[:blank:]\{1,\}\)\{2\}[^[:blank:]]\{1,\}\)\(.*\)[:blank:]NA/\1\3/
t a
' YourFile