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Shell Programming and Scripting

Output calculations

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# 1  
Old 01-27-2015
Output calculations
Attached are the is original output (zipped file) and a custom file using the awk code below in which the average reads per bait are calculated (average.txt)

Code:
  awk '{if(len==0){last=$4;total=$6;len=1;getline}if($4!=last){printf("%s\t%f\n", last, total/len);last=$4;total=$6;len=1}else{total+=$6;len+=1}}END{printf("%s\t%f\n", last, total/len)}' output.bam.hist.txt > average.txt

Is it possible to output the length of the bait, average # of reads, and the # calculated ...x coverage (3 of reads * 150/length)? Thank you Smilie.

Bait Length Reads Coverage
chr12:112884064-112884217 153 158.20915 155x (158*150)/153
output.bam.hist.zip (7.7 KB) 
average.txt (528 Bytes) 
# 2  
Old 01-27-2015
unless you give us a small sample input and output and describe in words whats going on, you are less likely to find help.
# 3  
Old 01-27-2015
The input file is attached. If I run the code below:

Code:
 awk '{if(len==0){last=$4;total=$6;len=1;getline}if($4!=last){printf("%s\t%f\n", last, total/len);last=$4;total=$6;len=1}else{total+=$6;len+=1}}END{printf("%s\t%f\n", last, total/len)}' output.bam.hist.txt > average.txt

a file called average.txt results that combines all the baita that match (chr....) and calculates the average # of reads.

The first three lines of average.txt:
Code:
chr12:112884064-112884217 158.2092
chr12:112888106-112888331 220.5333
chr12:112890983-112891206 228.287

The text is the bait followed by the average # of reads, in the input file each bait is outputted over and over again in different positions and thw script combines the baits that match and calculates the #'s of each.

Is it possible to output the length of the bait, average # of reads, and the # calculated ...x coverage (3 of reads * 150/length)? Thank you Smilie.
Code:
Bait                                Length Reads     Coverage
chr12:112884064-112884217 153 158.20915 155x (158*150)/153

the formula is not needed, I was just trying to show how the coverage is calculated.
output.bam.hist.txt (128.4 KB) 
Last edited by rbatte1; 01-28-2015 at 08:18 AM.. Reason: Added CODE tags
# 4  
Old 01-27-2015
Your input sample has non-printable CR characters, that obscures the output.
Here is a more straight awk code that also eliminates the CRs
Code:
awk '
function pr() {if (len>0) printf "%s\t%d\t%f\n", last, len, total/len}
{gsub("\r","")} # eliminate CRs
($4!=last) {
  pr()
  last=$4
  total=len=0
}
{total+=$6; len+=1}
END {pr()}
' output.bam.hist.txt > average.txt

---------- Post updated at 04:17 PM ---------- Previous update was at 03:51 PM ----------

You said "3 of reads". Looking at my US keyboard, you probably want "# of reads".
Then append another \t%f (tab character and a floating point field) to the first argument of the printf, and add another argument with the formula:
Code:
function pr() {if (len>0) printf "%s\t%d\t%f\t%f\n", last, len, total/len, total/len*150/len}

# 5  
Old 06-19-2015
Not sure what is wrong. Thank you very much Smilie.

Code:
$ awk '
>  function pr() {if (len>0) printf "%s\t%d\t%f\t%f\n", last, len, total/len}
>  function ar() {if (len>0) printf "%s\t%d\t%f\t%f\n", last, len, total/len, total/len*150/len}
>  {gsub("\r","")} # eliminate CRs
>  ($4!=last) {
>    pr()
>    last=$4
>    total=len=0
>  }
>  {total+=$6; len+=1}
>  END {pr()}
>  ' output.bam.hist.txt > average.txt
awk: cmd. line:2: (FILENAME=output.bam.hist.txt FNR=154) fatal: not enough arguments to satisfy format string
        `%s     %d      %f      %f
'
                  ^ ran out for this one

# 6  
Old 06-19-2015
Quote:
Originally Posted by cmccabe
Not sure what is wrong. Thank you very much Smilie.
Code:
printf "%s\t%d\t%f\t%f\n", last, len, total/len}

1 -> %s <- last
2 -> %d <- len
3 -> %f <- total/len
4 -> %f <- undefined
# 7  
Old 06-19-2015
This command runs: but does not result in the desired output, did I do something wrong? Thank you Smilie.

Code:
awk '
 function pr() {if (len>0) printf "%s\t%d\t%f\n", last, len, total/len}
 function ar() {if (len>0) printf "%s\t%d\t%f\t%f\n", last, len, total/len, total/len*150/len}
 {gsub("\r","")} # eliminate CRs
 ($4!=last) {
   pr()
   last=$4
   total=len=0
 }
 {total+=$6; len+=1}
 END {pr()}
 ' output.bam.hist.txt > average2.txt

Desired output
(in line 1 the equation for $4 would be (158*150) / 153 = 155x
the 150 is a static # that will never change
Code:
chr12:112884064-112884217 153 158.20915 155x
chr12:112888106-112888331 225 220.533333 147x
chr12:112890983-112891206 223 228.286996 153x

Thank you Smilie.
average2.txt (570 Bytes) 
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