mjhjmtu

I have a table with several hundred lines:

a1 
a2 
a3 
a4 
b1 
b2 
b3 
b4 
c1 
c2 
c3 
c4
... etc.

I want to return it in the following order:

a1
b1
c1
d1
a2
b2
c2
d2
a3
b3
c3

The script below works to select the first block of lines:

$ awk 'NR%4==1)print'

But how can I loop it to do it for the whole file?

You can use sort to do the sorting instead. Specifically you can tell sort to do a general sort, g which handles the sorting of letters and numbers. We can control which character in the string we want to do the sorting on by telling sort using the X.Y notation instead of the more typical X,Y notation.

For example:

$ sort -k1.2g file
a1
b1
c1
a2
b2
c2
a3
b3
c3
a4
b4
c4

Sort options:

 -k, --key=KEYDEF
 sort via a key; KEYDEF gives location and type
 -g, --general-numeric-sort
 compare according to general numerical value

 KEYDEF is F[.C][OPTS][,F[.C][OPTS]] for start and stop position, where F is
 a field number and C a character position in the field; both are origin 1,
 and the stop position defaults to the line's end. If neither -t nor -b is 
 in effect, characters in a field are counted from the beginning of the 
 preceding whitespace. OPTS is one or more single-letter ordering options
 [bdfgiMhnRrV], which override global ordering options for that key. If 
 no key is given, use the entire line as the key.

If the "step" is always small (in your case, 4) then a quick'n'dirty way might be to simply read the file that many times and pick out the records at each offset - e.g.

awk 'FNR==1 k++ !((FNR-k)%4)' file file file file
a1 
b1 
c1 
a2 
b2 
c2 
a3 
b3 
c3 
a4 
b4 
c4

or, equivalently, using GNU Awk (with its BEGINFILE rule):

gawk 'BEGINFILEk++ !((FNR-k)%4)' file file file file