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Top Forums Shell Programming and Scripting awk to output the percentage of a field compared to length Post 302956520 by cmccabe on Wednesday 30th of September 2015 04:10:17 PM
Old 09-30-2015
awk to output the percentage of a field compared to length

The awk below using the sample input would output the following: Basically, it averages the text in $5 that matches if $7 < 30 .
Code:
awk '{if(len==0){last=$5;total=$7;len=1;getline}if($5!=last){printf("%s\t%f\n", last, total/len);last=$5;total=$7;len=1}else{total+=$7;len+=1}}END{printf("%s\t%f\n", last, total/len)}' Input.txt > output.txt

Sample Input
Code:
chr 1   955542  955763  +   AGRN:exon.1 1   0 
chr1   955542  955763  +   AGRN:exon.1 2   0 
chr 1   955542  955763  +   AGRN:exon.1 3   0 
chr 1   955542  955763  +   AGRN:exon.1 4   1 
chr 1   955542  955763  +   AGRN:exon.1 5   1 
chr 1   955542  955763  +   AGRN:exon.1 6   1 
.... 
.... 
chr 1   955542  955763  +   AGRN:exon.1 218 32 
chr 1   955542  955763  +   AGRN:exon.1 219 32 
chr 1   955542  955763  +   AGRN:exon.1 220 32 
chr 1   955542  955763  +   AGRN:exon.1 221 29



Output

Code:
 AGRN:exon.1 4.5714285

My question is I can not seem to add the correct syntax that will also output the total # of lines in $6 that represent $5 and the % of 7 < 30 I know my words may not be all that helpful so hopefully the desired output will help. Thank you Smilie.


Desired output
Code:
  
ID             Average Reads      % of Baits 
AGRN:exon.1    4.5714285          3.16742     (221 (# of lines in $6 /   the # 0f lines < 30 in $7)


the boild is only to show the math and does not need rto be included.

Last edited by cmccabe; 09-30-2015 at 05:57 PM.. Reason: fixed formatting; [mod] extra code tags, added details
 

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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specifed in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. JOIN(1)
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