mjhjmtu

I have a file called "threewords". It contains the information:

#gray speedy bee

gr-A | sp-E-d-E | b-E

#gray greedy pea

gr-A | gr-E-d-E | p-E

When I run the command:

cat threewords | grep ^# | cut -c2-

The command pulls the two lines beginning with #. It then removes the # and returns this as output:

gray speedy bee

gray greedy pea

When I run my command:

array=($(cat threewords | grep ^# | cut -c2-))

It creates the array but it separates all the words into separate array positions like this:

array[0] = gray,
array[1] = speedy,
array[2] = bee,
array[3] = gray,
array[4] = greedy,
array[5] = pea

I can figure out the code to make it put the output of each line into an array like so:

array[0] = gray speedy bee, 
array[1] = gray greedy pea

The splitting is done with IFS as the delimiter (which contains a space, newline and tab by default). Set the IFS to only the newline:

$ IFS=$'n' a=($(printf "1 2n2 3n"))
$ echo $a[0]
1 2
$ echo $a[1]
2 3

This will change IFS for the shell, so best save it before and restore it:

OLD_IFS="$IFS"
IFS=$'n' array=($(grep '^#' threewords | cut -c2-))
IFS="$OLD_IFS"

And there's absolutely no reason to do:

cat threewords | grep '^#'

grep is perfectly capable of reading files:

grep '^#' threewords

As Stephane notes, when subjecting the output of a command to further shell expansion, one should disable globbing using set -f:

$ help set 
...
 -f Disable file name generation (globbing).

Otherwise:

$ cd /; a=( $(printf "*n") )
$ echo $a[@]
bin boot cdrom dev etc home ...

If you have bash 4

mapfile -t array < <(grep ^# threewords | cut -c2-)

Will populate array, one line per element

printf "%sn" "$array[@]"
gray speedy bee
gray greedy pea