I have a sting of "0"s and "1"s that I need to analyze. I need to look at each "1" and determine if it is in a neighborhood that is enriched for "1"s which means it is one of at least three "1"s in a 4 character window. My desired output is a count of "1"s in an enriched area.
For Example
Input sequence= 0100101000111011010111000
Output = 9
SO far my code looks like the following:
Code:
echo $string
length=$(echo ${#string})
rlength=$[$length-3]
i=3
count=0
while [ $i -lt $rlength ];
do
res=$(echo ${string:$[$i]:1})
if [ $[$res] -eq "1" ]
then
if [ $[$(echo ${string:$[$i-3]:1}) + $(echo ${string:$[$i-2]:1}) + $(echo ${string:$[$i-1]:1}) ] -ge "2" ]
then
count=$[$count+1]
elif [ $[$(echo ${string:$[$i-3]:1}) + $(echo ${string:$[$i-2]:1}) + $(echo ${string:$[$i-1]:1}) ] -ge "2" ]
then
count=$[$count+1]
elif [ $[$(echo ${string:$[$i-3]:1}) + $(echo ${string:$[$i-2]:1}) + $(echo ${string:$[$i-1]:1}) ] -ge "2" ]
then
count=$[$count+1]
elif [ $[$(echo ${string:$[$i-3]:1}) + $(echo ${string:$[$i-2]:1}) + $(echo ${string:$[$i-1]:1}) ] -ge "2" ]
then
count=$[$count+1]
fi
fi
i=$[$i+1]
done
echo $count
It works just fine but problems include:
1) that, most importantly, it is slow as a snail.
2) it misses the first 3 characters of the string and the last three. I could live with this if necessary as long as the rest of the code works more quickly.
Any and all suggestions are welcome. Please understand that I am still new to this and description of what suggested code is doing is really, really useful.
Last edited by monstrousturtle; 05-14-2012 at 03:18 PM..
Reason: clarity of the code
{
for (i=1;i<=NF;i++) {
if ($i==1) {
for (j=1;j<=4;j++) {
ones=0;
for (k=(i+j-4);k<=(i+j-1);k++) {
if (k>0) {
if ($k==1) {
ones++;
}
if (ones>=3) {
e[i]=1;
}
}
}
}
}
}
}
END{for (i in e) count++;print count}
Then run:
Code:
echo $string | awk -vFS="" -f script.awk
BTW, your script is giving "6" for this sample input...
Last edited by bartus11; 05-14-2012 at 04:13 PM..
Reason: fixed for first three characters
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