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awk calculation with zero as N/A

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Top Forums Shell Programming and Scripting awk calculation with zero as N/A
# 8  
Old 05-23-2016
But isn't he or she calculating (1-f1[$1]/$3)? With $1 == ABHD12, f1["ABHD12"] == 10 (from file1), so the result should be around 1 - 0,015 = 0.985, shouldn't it?
This User Gave Thanks to RudiC For This Post:
cmccabe
# 9  
Old 05-23-2016
I need to clean-up the data a bit more and will post back tomorrow. Thank you very much Smilie.
# 10  
Old 05-23-2016
I think part of my problem is that in the attached files, using the awk below Iam getting the correct counts for most of the ids. However, in cases like RYK I get an output of 250 in $2, but if I manually look at each of the files I count 259 in $2.

awk
Code:
awk '{A[$3] += $2} END{for (i in A) print i, A[i]}' NA12878_newheader_base_counts_lessthan_30reads_perbase_lessthan_genes.txt (file1) NS12911_newheader_base_counts_lessthan_30reads_perbase_lessthan_genes.txt(file2) > all_genes_bases.txt

files.tar.gz (1.05 MB) 
# 11  
Old 05-24-2016
Quote:
Originally Posted by cmccabe
I think part of my problem is that in the attached files, using the awk below Iam getting the correct counts for most of the ids. However, in cases like RYK I get an output of 250 in $2, but if I manually look at each of the files I count 259 in $2.

awk
Code:
awk '{A[$3] += $2} END{for (i in A) print i, A[i]}' NA12878_newheader_base_counts_lessthan_30reads_perbase_lessthan_genes.txt (file1) NS12911_newheader_base_counts_lessthan_30reads_perbase_lessthan_genes.txt(file2) > all_genes_bases.txt

I'm confused...

You ask us to download over a megabyte of data in a gzipped tar file that contains two files:
Code:
NA12878_newheader_base_counts_lessthan_30reads_perbase.bed
NS12911_newheader_base_counts_lessthan_30reads_perbase.bed

Neither of which are referenced by the above above code (even after removing the parenthetical elements from the file list).
And, if we change the script above to:
Code:
awk '{A[$3] += $2} END{for (i in A) print i, A[i]}' NA12878_newheader_base_counts_lessthan_30reads_perbase.bed NS12911_newheader_base_counts_lessthan_30reads_perbase.bed > all_genes_bases.txt

the output produced is never going to have anything with an alphabetic string in the 1st output field because neither of these input file contain any alphabetic characters in their third fields.

Please explain what is going on here!
This User Gave Thanks to Don Cragun For This Post:
cmccabe
# 12  
Old 05-24-2016
added ICODE tags
I apologize for the confusion and will post back in a bit with a better example. Part of the issue that I am having, besides the zero line after most cases, is that some of the initial calculations are incorrect. The awk posted works for most but not all. Again I apologize and will post better examples with an explanation. Thank you Smilie.

---------- Post updated at 08:03 AM ---------- Previous update was at 05:16 AM ----------

I believe I found my error on the miscalculation issue I was having in the above confusing post. I am not sure why in the output there are leading and trailing zero's or how to fix that. As you suspected that is happening but why is a mystery to me Smilie. Thank you Smilie.

current output
Code:
0
0
0
0
0
0
0
0
0
0
0
AASS 99.26%
0
0
ABCA10 97.61%
0
ABCA12 99.97%

desired output
Code:
AASS 99.26%
ABCA10 97.61%
ABCA12 99.97%

files used to calculate those:
file1
Code:
AASS 24
ABCA10 103
ABCA12 3

file2
Code:
AASS 23 3241
ABCA10 28 4301
ABCA12 52 8804

calculation math:
$1 in is matched to $1 of file2 and the file1 $2 / the file2 $3 x 100 =x
100 - x = %

example
Code:
AASS  24/3241 x 100 = 0.74
100 - 0.74 = 99.26%

# 13  
Old 05-24-2016
Hello cmccabe,

Could you please try following and let me know if this helps.
Code:
awk 'FNR==NR{A[$1]=$2;next} ($1 in A){X=(A[$1]/$3)*100;printf("%s %.2f\n",$1,  100-X)}' file1 file2

Output will be as follows.
Code:
AASS 99.26
ABCA10 97.61
ABCA12 99.97

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 14  
Old 05-24-2016
works great.... thank you very much Smilie.
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