Getting output of shell command in bash array

To build the associative array, try this:

declare -A proVarwhile read -r val key; do  proVar[${key#chr}]=$valdone < <(awk '{printf ("%s\t\n"), $1}' file.txt | grep -P 'pattern' | uniq -c)

^{Note: This assumes that your command's output is composed of multiple lines, each containing one key-value pair; the single-line output shown in your question comes from passing $proVar to echo without double quotes.}

• Uses a while loop to read each output line from a process substitution (<(...)).
• The key for each assoc. array entry is formed by stripping prefix chr from each input line's first whitespace-separated token, whereas the value is the rest of the line (after the separating space).

To then create the bar plot, use:

while IFS= read -r key; do  echo "chr${key} $(printf '=%.s' $(seq $(( ${proVar[$key]} / 50 ))))"done < <(printf '%s\n' "${!proVar[@]}" | sort -n)

^{Note: Using sort -n to sort the keys will put non-numeric keys such as X and Y before numeric ones in the output.}

• $(( ${proVar[$key]} / 50 )) calculates the number of = chars. to display, using integer division in an arithmetic expansion.
• The purpose of $(seq ...) is to simply create as many tokens (arguments) as = chars. should be displayed (the tokens created are numbers, but their content doesn't matter).
• printf '=%.s' ... is a trick that effectively prints as many = chars. as there are arguments following the format string.
• printf '%s\n' "${!proVar[@]}" | sort -n sorts the keys of the assoc. array numerically, and its output is fed via a process substitution to the while loop, which therefore iterates over the keys in sorted order.

You can create an array in an assignment using parentheses:

proVar=(`awk '{printf ("%s\t\n"), $1}' file.txt | grep -P 'pattern' | uniq -c`)

There's no built-in way to create an associative array directly from input. For that you'll need an additional loop.