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Full Discussion: Perl- Finding average "frequency" of occurrence of duplicate lines
Top Forums Shell Programming and Scripting Perl- Finding average "frequency" of occurrence of duplicate lines Post 302545611 by acsg on Tuesday 9th of August 2011 02:17:10 AM
Old 08-09-2011
Quote:
Originally Posted by yazu
I believe it is possible. But I'm not sure I understand the task (sorry, English is not my native language). Please give examples of your input and the desired output. Maybe it would be enough if you give the desired output for my INPUTFILE:
All lines: 9
Lines between a: 1, 2, 0 (or maybe you need to remember line numbers - 1, 3, 6, 7?) so what output?
b: 2 - ?
c: ? (only one occurrence) - ?
d: 0 - ?


Thanks for your reply.
Yeah what I want is something like what you said. So, for your example input file, the output would be:

Code:
a- 4 2 
b- 2 3
c- 1 0
d- 2 1



the first field being the contents of the line being repeated, the second field the number of times found in the file, the third field being the average of "every how many lines it is repeated". So for example for 'a', first it appears after 2 lines, then 3 lines then 1 line. So the average of this makes 2 lines. Then for 'b' and 'd' since they are only duplicated once, there won't be a need to make an average. And, since 'c' is never repeated, then the average is just '0' (or could be blank, it doesn't matter).

On the other hand, how about keeping track of the timestamp and subtracting it to make the "time between repetitions" and then making an average? That was my original idea but I don't know how to keep track of this time, per each repeated line. The output in this case would be something like:

Code:
a- 4 0.05
b- 2 0.89
c- 1 0
d- 2 0.06



the last field being the seconds.

Thanks!
 

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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)
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