Shell Programming and Scripting

Hi.. I am in help of displaying this specific case. I have multiple files where i have to display accordingly.

Input file


First i have to remove the ##INFO lines and just display the columns
Second , i need to parse all the columns which ends with .bam .. there are hundreds of such columns. In these columns, there are 5 values seperated by ":" i wanted to display only first values i.e for example if a field looks like "0/0:0,42,253:14:0:45" , i wanted to display only "0/0"

Output

Code:

#!/usr/bin/perl -w 
 
while(<>){                             
next if(substr $_,0,2) eq '##'; 
    @a=split(/\s+/,$_);   
                           
for($i=0;$i<@a;$i++){   
    $a[$i]=~s/^(\d+\/\d+):.+/$1/; 
    if($i!=$#a){print"$a[$i]    "} 
    else{print"$a[$i]\n"}  
} 
}

syntax: ./script filename

Code:

# /^##/ {next}            # Skip lines starting with ##
# !/^#/ { ... } 1         # Process all lines not starting with # and print EVERY line
# gsub(/"[^ :]*/, "");    # Delete all instances of :..., stopping at spaces or colons

$ awk '/^##/{next}; !/^#/ { gsub(/:[^ :]*/, "") } 1' data

#CHROM POS INFO 57.sorted.bam 58.sorted.bam 59.sorted.bam 34.sorted.bam 55.sorted.bam
12 59 DP=157;VDB=0.0005;AF1=0.203;AC1=19;DP4=72,57,9,9; 0/0 0/0 0/0 0/0 0/0
12 68 DP=156;VDB=0.0002;AF1=0.4985;G3=8.399e-06,1,1.307e-05; 0/1 0/1 0/1 0/1 0/1
12 72 DP=160;VDB=0.0003;AF1=0.5132;G3=3.712e-06,1,1.79e-05; 0/1 0/1 0/1 0/1 0/1
12 99 DP=164;VDB=0.0002;AF1=0.5142;G3=3.45e-06,1,1.806e-05; 0/1 0/1 0/1 0/1 0/1
12 100 DP=164;VDB=0.0002;AF1=0.5124;G3=3.882e-06,1,1.781e-05; 0/1 0/1 0/1 0/1 0/1

$

perl script worked great.. thankyou
for some reason awk is giving out errors

Since you didn't say what errors I'm left trying to guess, but maybe your version of awk doesn't have gsub. Try 'nawk', that's where systems that don't have a good default awk hide the real version.

can be done in a single command line actualy
just didn't notice that there's no more : anywhere

Code:

perl -nle 'next if(substr $_,0,2) eq "##";s/:\d.+?(\s|$)/ /g;print' datafile

Good day geeks,
I also want to filter out some details in a specific file shown below:

==================================================================================================
Month: Mar Failure Ratio Key Performance Indicators (KPIs) NodeType: sgsn_g

Day Time Attach PDP Activation Intra SGSN RAU ISRAU Paging Cut-off
==================================================================================================
20 12.00 0.1% 0.0% 5.5% 0.0% 9.7% 0.1%
--------------------------------------------------------------------------------------------------
20 11.00 0.2% 0.0% 5.4% 0.3% 9.5% 0.2%
--------------------------------------------------------------------------------------------------
20 10.00 0.3% 0.0% 5.2% 0.2% 8.5% 0.1%
--------------------------------------------------------------------------------------------------
20 09.00 0.2% 0.0% 4.8% 1.0% 6.6% 0.3%
--------------------------------------------------------------------------------------------------
20 08.00 0.3% 0.0% 4.2% 0.5% 4.2% 0.6%
--------------------------------------------------------------------------------------------------
Average: 0.2% 0.0% 5.0% 0.4% 7.7% 0.3%


What i want to do is just to display only the headers (Month: Mar Failure Ratio Key Performance Indicators (KPIs) NodeType: sgsn_g
Day Time Attach PDP Activation Intra SGSN RAU ISRAU Paging Cut-off) and also the last part (Average). So that the output will come out as this:

Month: Mar Failure Ratio Key Performance Indicators (KPIs) NodeType: sgsn_g

Day Time Attach PDP Activation Intra SGSN RAU ISRAU Paging Cut-off


Average: 0.2% 0.0% 5.0% 0.4% 7.7% 0.3%



Geeks, am not lazy but i have been trying to use GREP, CUT but to no avail, i just started Shell Programming and i need to get this done fast. Please any help will be appreciated and if you have any good guide to Shell Programming please do give me an hint.

Thanks