I am using the following code to analyze a sequence by seqtk and use the output in awk to print total number of nucleotides and nucleotides marked as N.
seqtk comp "$FILE" | awk '{x+=$2}END{print "Total Nucleotides: " x}'
seqtk comp "$FILE" | awk '{x+=$9}END{print "Total Unknown Nucleotides: " x}'
seqtk comp "$FILE" | awk '{x+=$9 ; y+=$2}END{print "Percent of Unknown Nucleotides: " (x/y)*100}'
Since in the above code seqtk calculations are done 3 times, I want to process once and put the result in a variable and reuse. I have tried the following.
RESULT= seqtk comp "$FILE"
echo "$RESULT" | awk '{x+=$2}END{print "Total Nucleotides: " x}'
echo "$RESULT" | awk '{x+=$9}END{print "Total Unknown Nucleotides: " x}'
echo "$RESULT" | awk '{x+=$9 ; y+=$2}END{print "Percent of Unknown Nucleotides: " (x/y)*100}'
But the value of x comes out equal to 0.
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written
by
nadarajan_v •
use the -v option of awk:
awk -v awk_var=<your bash var>
awk -v x=$RESULT in your specific case
I tried the following
awk -v x= $RESULT '{x+=$2}END{print "Total Nucleotides: " x}'
It didn't produce any output.
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written
by
nadarajan_v •
there should be no space behind the x= part
also check if $RESULTS is correctly set (also there should be no space behind the = sign)
The $RESULT variable is empty. Not sure why.
did you remove the space after RESULT= in your cmdline?
moreover, you need to either use the backtick operator: `
or more modern the $() operator. eg RESULT=$(seqtk comp "$FILE")
After adding $() operator now $RESULT is set correctly. However, now I am getting this error: awk: cannot open 11820664 (No such file or directory). I have tried awk -v x=$RESULT '{print "Total Nucleotides: " x[2]}' as well as awk -v x=$RESULT '{x=$2}END{print "Total Nucleotides: " x}'. 11820664 is the third value in the line of data. Thanks
Finally, I made it to work by using the following code: awk '{x=$2}END{print "Total Nucleotides: " x}' <<< "$RESULT"
ok, if the 'value' of RESULTS is something multiline, it's all a bit more tricky.
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