Perl- Finding average "frequency" of occurrence of duplicate lines
Hello,
I am working with a perl script that tries to find the average "frequency" in which lines are duplicated. So far I've only managed to find the way to count how many times the lines are repeated, the code is as follows:
Code:
perl -ae'
my $filename= $ENV{'i'};
open (FILE, "$filename") or die $!;
my %seen= ();
while(my $line = <FILE>){
my @fields = split(/\s+/, $line);
my @fields2= @fields[3..16];
my $niin= join("\t", @fields2);
$seen{$niin}++;
}
foreach my $keys (sort {$seen{$b} <=> $seen{$a}} keys %seen){
print "$keys = $seen{$keys}\n";
}
close (FILE);
'
Now, what I want to do is find a way to find out the number of (in average) "every how many lines a certain line is repeated". So I was wondering if it's possible to have some sort of record and then in the end just calculate the average?
I actually have another way to calculate this frequency. In the original file being read, the first field is a unix timestamp (which i "cut out" for the counting of the duplicate lines). So I thought it would be possible as well to try to keep a record of the "time between repetitions" and then make an average in the end. Of course this would imply keeping a record for each duplicate line, which seems like a rather intricate operation. An example of the lines is :
Hi Friends,
Can any of you explain me about the below line of code?
mn_code=`env|grep "..mn"|awk -F"=" '{print $2}'`
Im not able to understand, what exactly it is doing :confused:
Any help would be useful for me.
Lokesha (4 Replies)
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******************
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Discussion started by: penchev
3 Replies
LEARN ABOUT DEBIAN
bp_oligo_count
BP_OLIGO_COUNT(1p) User Contributed Perl Documentation BP_OLIGO_COUNT(1p)NAME
oligo_count - oligo count and frequency
SYNOPSIS
Usage: oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
[-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
[-o/--out OUTFILE]
DESCRIPTION
This scripts counts occurrence and frequency for all oligonucleotides of given length.
It can be used to determine what primers are useful for frequent priming of nucleic acid for random labeling.
Note that this script could be run by utilizing the compseq program which is part of EMBOSS.
OPTIONS
The default sequence format is fasta. If no outfile is given, the results will be printed to standard out. All other options can entered
interactively.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Charles C. Kim
Email cckim@stanford.edu
HISTORY
Written July 2, 2001
Submitted to bioperl scripts project 2001/08/06
>> 100 x speed optimization by Heikki Lehvaslaiho
perl v5.14.2 2012-03-02 BP_OLIGO_COUNT(1p)
08-09-2011
