Here is my AWK script to find the root mean square deviation of a set of data coming as a 51 column data file. I am reading each column of data *relative* to the last column ($51)
How could I get AWK to automatically detect the number of columns and use it as a reference. I.e. is there a way of making the script smoother.
Currently I also rely on 50 variables s_0, s_1, s_2, ..., s_50
how could I write this as an increment too. I really want to make the script more logical.
Code:
BEGIN {s_0=0;n_0=0}
{n_0++;s_0+=($51-$1)^2}
END {print sqrt(s_0/n_0)}
BEGIN {s_1=0;n_1=0}
{n_1++;s_1+=($51-$2)^2}
END {print sqrt(s_1/n_1)}
BEGIN {s_2=0;n_2=0}
{n_2++;s_2+=($51-$3)^2}
END {print sqrt(s_2/n_2)}
BEGIN {s_3=0;n_3=0}
{n_3++;s_3+=($51-$4)^2}
END {print sqrt(s_3/n_3)}
BEGIN {s_4=0;n_4=0}
{n_4++;s_4+=($51-$5)^2}
END {print sqrt(s_4/n_4)}
BEGIN {s_5=0;n_5=0}
{n_5++;s_5+=($51-$6)^2}
END {print sqrt(s_5/n_5)}
BEGIN {s_6=0;n_6=0}
{n_6++;s_6+=($31-$7)^2}
END {print sqrt(s_6/n_6)}
BEGIN {s_7=0;n_7=0}
{n_7++;s_7+=($51-$8)^2}
END {print sqrt(s_7/n_7)}
BEGIN {s_8=0;n_8=0}
{n_8++;s_8+=($51-$9)^2}
END {print sqrt(s_8/n_8)}
BEGIN {s_9=0;n_9=0}
{n_9++;s_9+=($51-$10)^2}
END {print sqrt(s_9/n_9)}
BEGIN {s_10=0;n_10=0}
{n_10++;s_10+=($51-$11)^2}
END {print sqrt(s_10/n_10)}
BEGIN {s_11=0;n_11=0}
{n_11++;s_11+=($51-$12)^2}
END {print sqrt(s_11/n_11)}
BEGIN {s_12=0;n_12=0}
{n_12++;s_12+=($51-$13)^2}
END {print sqrt(s_12/n_12)}
BEGIN {s_13=0;n_13=0}
{n_13++;s_13+=($51-$14)^2}
END {print sqrt(s_13/n_13)}
BEGIN {s_14=0;n_14=0}
{n_14++;s_14+=($51-$15)^2}
END {print sqrt(s_14/n_14)}
BEGIN {s_15=0;n_15=0}
{n_15++;s_15+=($51-$16)^2}
END {print sqrt(s_15/n_15)}
BEGIN {s_16=0;n_16=0}
{n_16++;s_16+=($51-$17)^2}
END {print sqrt(s_16/n_16)}
BEGIN {s_17=0;n_17=0}
{n_17++;s_17+=($51-$18)^2}
END {print sqrt(s_17/n_17)}
BEGIN {s_18=0;n_18=0}
{n_18++;s_18+=($51-$19)^2}
END {print sqrt(s_18/n_18)}
BEGIN {s_19=0;n_19=0}
{n_19++;s_19+=($51-$20)^2}
END {print sqrt(s_19/n_19)}
BEGIN {s_20=0;n_20=0}
{n_20++;s_20+=($51-$21)^2}
END {print sqrt(s_20/n_20)}
BEGIN {s_21=0;n_21=0}
{n_21++;s_21+=($51-$22)^2}
END {print sqrt(s_21/n_21)}
.......
.......
BEGIN {s_49=0;n_49=0}
{n_49++;s_49+=($51-$50)^2}
END {print sqrt(s_49/n_49)}
BEGIN {s_50=0;n_50=0}
{n_50++;s_50+=($51-$51)^2}
END {print sqrt(s_50/n_50)}
The script outputs 51 RMSD values, one for each column.
awk '
{
for(i=1; i<NF; i++) # from 1..50
{ n=1 # same as n=0; n++
arr[i]=sqrt( ( ($51 - $i)^2 )/n) # you could use xxx /1 as well
print arr[i];
}
} ' inputfile
This does what you coded, but uses an array arr[], and a loop.
{
for(i=1; i<NF; i++) # from 1..50
{ n=1 # same as n=0; n++
arr[i]=sqrt( ( ($51 - $i)^2 )/n) # you could use xxx /1 as well
print arr[i];
}
}
My old script would evaluate all data in a column relative to $51, and output only a *single* RMSD value for that operation. i.e. I was left with 50 RMSD values. Yours outputs thousands of lines of RMSDs, I suspect we are not doing the same thing.
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