Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

awk to average target and gene

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting awk to average target and gene
# 1  
Old 07-28-2015
awk to average target and gene
I am trying to modify the awk below to include the gene name ($5) for each target and can not seem to do so. Also, I'm not sure the calculation is right (average of all targets that are the same is $4 using the values in $7)? Thank you Smilie.

Code:
awk '{if((NR>1)&&($4!=last)){printf("%s\t%f\t%s\n", last,  total/len,pg);total=$7;len=1;}else{total+=$7;len+=1};pg=$5;last=$4;}END{printf("%s\t%f\t%s\n",  last, total/len,pg)}'

output.bam.hist.txt
Code:
chr1    40539722    40539865    chr1:40539722-40539865    PPT1    1    159
chr1    40539722    40539865    chr1:40539722-40539865    PPT1    2    161
chr1    40539722    40539865    chr1:40539722-40539865    PPT1    3    161

epilepsy70_average.txt
Code:
chr1:40539722-40539865    72.000000
chr1:40542503-40542595    46.500000
chr1:40544221-40544340    60.000000

Desired epilepsy70_average.txt
Code:
chr1:40539722-40539865    72.000000      PPT1
chr1:40542503-40542595    46.500000      PPT1
chr1:40544221-40544340    60.000000      PPT1

EDIT: I have modified the awk to calculate average using $7 and include $5 in the output below.

epilepsy70_average.txt
Code:
chr1:40539722-40539865    227.776224    PPT1
chr1:40542503-40542595    109.706522    PPT1
chr1:40544221-40544340    61.596639    PPT1

I can not figure out if the calculated value in $2 is less than or equal to 100 then that line the font changed to red, then the entire file is sort in ascending order by $2 Is this possible?

I think the below will print and maybe thats a start:

Code:
 awk '{if((NR>1)&&($4!=last)){printf("%s\t%f\t%s\n", last,  total/len,pg);total=$7;len=1;}else{total+=$7;len+=1};pg=$5;last=$4;}END{printf("%s\t%f\t%s\n",  last, total/len,pg)}' | awk '{if($2>=1000.00)print;}' epilepsy70_average.txt > sort.txt

Last edited by cmccabe; 07-29-2015 at 11:03 AM.. Reason: edited code to calulate from $7 and include $5
# 2  
Old 07-31-2015
I find multi-line scripts better readable.
A delayed printing (that happens by condition in the loop and in the END section) is better to be defined once in a function.
Code:
#!/bin/sh
awk '
function prt(){ printf "%s\t%f\t%s\n", last, total/len, pg }
{
  if (NR>1 && $4!=last) {
    prt()
    total=0; len=0
  }
  total+=$7; len+=1
  pg=$5
  last=$4
}
END { prt() }
' "$@" |

awk '{ if ($2>=100) print }' |

sort -k2,2n

Note the -k2,2n to sort on field 2.
The "$@" passes arguments, so you can run the script with
Code:
./scriptname file

Of course you can also do
Code:
./scriptname < file

Now if you want to optimize the two awk scripts into one, you can change the prt function:
Code:
#!/bin/sh
awk '
function prt(){
  avg=total/len
  if (avg>=100) {
    printf "%s\t%f\t%s\n", last, avg, pg
  }
}
{
  if (NR>1 && $4!=last) {
    prt()
    total=0; len=0
  }
  total+=$7; len+=1
  pg=$5
  last=$4
}
END { prt() }
' "$@" |

sort -k2,2n

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk Moving Average

Hi, I'm using awk to try and get a moving average for the second column of numbers ($2) in the below example broken out by unique identifier in column 1 ($1) : H1,1.2 H1,2.3 H1,5.5 H1,6.6 H1,8.7 H1,4.1 H1,6.4 H1,7.8 H1,9.6 H1,3.2 H5,50.1 H5,54.2 H5,58.8 H5,60.9 H5,54.3 H5,52.7... (8 Replies)
Discussion started by: theflamingmoe
8 Replies

2. Shell Programming and Scripting

Average across multiple columns - awk

Hi forum members, I'm trying to get an average of multiple columns in a csv file using awk. A small example of my input data is as follows: cu,u3o8,au,ag -9,20,-9,3.6 0.005,30,-9,-9 0.005,50,10,3.44 0.021,-9,8,3.35 The following code seems to do most of what I want gawk -F","... (6 Replies)
Discussion started by: theflamingmoe
6 Replies

3. Shell Programming and Scripting

awk to output id, location, and average

Trying to use awk output the target in $1 with the region it maps to in $2 along with its average. The below is close but I just can not seem to add the region it maps to or get the count of lines not of the text. Thank you :). Basically, $1 occurs 5 times and maps to $2 with an average... (2 Replies)
Discussion started by: cmccabe
2 Replies

4. Shell Programming and Scripting

awk or Bash: Cumulative average

For the data I would like to parse down and for each parsing I want a cumulative averaging, stored in an array that can be output. I.e. 546/NR = 546 (546+344)/NR=(546+344)/2 = etc. For N record input I want N values of the average (a block averaging effectively) Any... (3 Replies)
Discussion started by: chrisjorg
3 Replies

5. HP-UX

After adding new iscsi target port, still the session state of that target port is showing offline

Hi, I wanted to configure new iscsi port on HPUX system, i added the target port address and configured it, once done, went to array side and searched for that host iqn number , but was nt able to find the same, came to host, then when i ran "iscsiutil -pVS" command it gave me below result ... (0 Replies)
Discussion started by: Vinay Kumar D
0 Replies

6. Shell Programming and Scripting

Calculating average with awk

I need to find the average from a file like: data => BW:123 M:30 RTD:0 1 0 1 0 0 1 1 1 1 0 0 1 1 0' data => BW:123 N:30 RTD:0 1 0 1 0 0 1 1 1 1 0 0 1 1 0' data => BW:123 N:30 RTD:0 1 0 1 0 0 1 1 1 1 0 0 1 1 0' data => BW:123 N:30 RTD:0 1 0 1 0 0 1 1 1 1 0 0 1 1 0' data => BW:123 N:30 RTD:0 1... (4 Replies)
Discussion started by: Slagle
4 Replies

7. Shell Programming and Scripting

Calculate Average AWK

I want to calculate the average line by line of some files with several lines on them, the files are identical, just want to average the 3rd columns of those files.:wall: Example file: File 1 001 0.046 0.667267 001 0.047 0.672028 001 0.048 0.656025 001 0.049 ... (2 Replies)
Discussion started by: AriasFco
2 Replies

8. Shell Programming and Scripting

Partial average of a column with awk

Hello, Let's assume I have 100 files FILE_${m} (0<m<101). Each of them contains 100 lines and 10 columns. I'd like to get in a file called "result" the average value of column 3, ONLY between lines 11 and 17, in order to plot that average as a function of the parameter m. So far I can compute... (6 Replies)
Discussion started by: DMini
6 Replies

9. Shell Programming and Scripting

Average in awk

Hi I am looking for an awk script which can compute average of all the fields every 5th line. The file looks: A B C D E F G H I J K L M 1 18 13 14 12 14 13 11 12 12 15 15 15 2 17 17 13 13 13 12 12 11 12 14 15 14 3 16 16 12 12 12 11 11 12 11 16 14 13 4 15 15 11 11 11 12 11 12 11... (6 Replies)
Discussion started by: saint2006
6 Replies

10. Shell Programming and Scripting

how to average in awk

Hi, I have the data like this $1 $2 1 12 2 13 3 14 4 12 5 12 6 12 7 13 8 14 9 12 10 12 i want to compute average of $1 and $2 every 5th line (1-5 and 6-10) Please help me with awk Thank you (4 Replies)
Discussion started by: saint2006
4 Replies
Login or Register to Ask a Question