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Full Discussion: Duplication | awk | result
Top Forums UNIX for Beginners Questions & Answers Duplication | awk | result Post 303036036 by Aurimas on Thursday 13th of June 2019 05:40:33 AM
Old 06-13-2019
Thank you. Also I have another question. Basically for the input file (calculate_contacts_HS_*.pdb.txt) I want that all lines that have ALA in first or second column sum the third column numerical values of those lines. In the input file given below it would have to be 3 lines that contain ALA in 2nd column (but it can also be in 1st) and 3rd column summed would be: 1.32859+6.90889+0.0962809=8.333761. The example of input file is this:

Code:
c<B>r<3>a<2300>R<LEU>A<CD1> c<B>r<56>a<2643>R<ALA>A<N> 1.32859 4.26827 . .
c<B>r<3>a<2300>R<LEU>A<CD1> c<B>r<56>a<2644>R<ALA>A<CA> 6.90889 4.0211 . .
c<B>r<3>a<2300>R<LEU>A<CD1> c<B>r<56>a<2646>R<ALA>A<O> 0.0962809 4.95892 . .

and the script is this:

Code:
#!/bin/bash
read -p "amino acid: " AAA
if [[ "ALA ARG ASN ASP CYS GLN GLY GLU HIS ILE \
	   LEU LYS MET PHE PRO SER THR TRP TYR VAL" =~ $AAA ]]
then 
	for i in calculate_contacts_HS_*.pdb.txt; 
		do
			awk '{ if ($0 ~ /$AAA/) sum += $3} END {print sum}' $i
        done
else
	exit 1
fi

but for this script I don't get any value. When I run the script through command the output I get is this:
Code:

Because in my script AAA is assigned to one of the 20 values (ALA, ASN, ARG, ASP, CYS, GLU, GLN, LEU, ILE, LYS, MET, etc.) therefore $AAA can be assigned to different values, but for this case let's assume that $AAA = ALA.

I will look forward to your responses.

Sincerely,
Aurimas

Last edited by Aurimas; 06-13-2019 at 07:40 AM..
 

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TOTAL(1)						      General Commands Manual							  TOTAL(1)

NAME
total - sum up columns SYNOPSIS
total [ -m ][ -sE | -p | -u | -l ][ -i{f|d}[N] ][ -o{f|d} ][ -tC ][ -N [ -r ]] [ file .. ] DESCRIPTION
Total sums up columns of real numbers from one or more files and prints out the result on its standard output. By default, total computes the straigt sum of each input column, but multiplication can be specified instead with the -p option. Likewise, the -u option means find the upper limit (maximum), and -l means find the lower limit (minimum). Sums of powers can be computed by giving an exponent with the -s option. (Note that there is no space between the -s and the exponent.) This exponent can be any real number, positive or negative. The absolute value of the input is always taken before the power is computed in order to avoid complex results. Thus, -s1 will produce a sum of absolute values. The default power (zero) is interpreted as a straight sum without taking absolute values. The -m option can be used to compute the mean rather than the total. For sums, the arithmetic mean is computed. For products, the geomet- ric mean is computed. (A logarithmic sum of absolute values is used to avoid overflow, and zero values are silently ignored.) If the input data is binary, the -id or -if option may be given for 64-bit double or 32-bit float values, respectively. Either option may be followed immediately by an optional count, which defaults to 1, indicating the number of double or float binary values to read per record on the input file. (There can be no space between the option and this count.) Similarly, the -od and -of options specify binary double or float output, respectively. These options do not need a count, as this will be determined by the number of input channels. A count can be given as the number of lines to read before computing a result. Normally, total reads each file to its end before producing its result, but this behavior may be overridden by inserting blank lines in the input. For each blank input line, total produces a result as if the end-of-file had been reached. If two blank lines immediately follow each other, total closes the file and proceeds to the next one (after reporting the result). The -N option (where N is a decimal integer) tells total to produce a result and reset the calculation after every N input lines. In addition, the -r option can be specified to override reinitialization and thus give a running total every N lines (or every blank line). If the end of file is reached, the current total is printed and the calculation is reset before the next file (with or without the -r option). The -tC option can be used to specify the input and output tab character. The default tab character is TAB. If no files are given, the standard input is read. EXAMPLE
To compute the RMS value of colon-separated columns in a file: total -t: -m -s2 input To produce a running product of values from a file: total -p -1 -r input BUGS
If the input files have varying numbers of columns, mean values will certainly be off. Total will ignore missing column entries if the tab separator is a non-white character, but cannot tell where a missing column should have been if the tab character is white. AUTHOR
Greg Ward SEE ALSO
cnt(1), neaten(1), rcalc(1), rlam(1), tabfunc(1) RADIANCE
2/3/95 TOTAL(1)
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