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Full Discussion: awk to count condition in field
Top Forums Shell Programming and Scripting awk to count condition in field Post 302962175 by Aia on Wednesday 9th of December 2015 11:06:35 AM
Old 12-09-2015
Quote:
Originally Posted by protocomm
in the spirit of cmccabe:

Code:
awk '$8=="snp"{a++};$8=="ins"{b++};$8=="del"{c++}END{print "snp="a "\n" "ins="b "\n" "del="c}'

$8 appears to contain the string TYPE=snp, etc..., therefore that would not do. Perhaps:

Code:
awk '$8 ~ /snp/ {a++} $8 ~ /ins/ {b++} $8 ~ /del/ {c++}END{print "snp="a "\n" "ins="b "\n" "del="c}'

This User Gave Thanks to Aia For This Post:
cmccabe
 

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LEARN ABOUT DEBIAN

bio::variation::snp

Bio::Variation::SNP(3pm)				User Contributed Perl Documentation				  Bio::Variation::SNP(3pm)

NAME

       Bio::Variation::SNP - submitted SNP

SYNOPSIS

	 $SNP = Bio::Variation::SNP->new ();

DESCRIPTION

       Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs,
       batch IDs, validation methods).

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 one
       of the Bioperl mailing lists. Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Allen Day <allenday@ucla.edu>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   get/set-able methods
	Usage	: $is = $snp->method()
	Function: for getting/setting attributes
	Returns : a value.  probably a scalar.
	Args	: if you're trying to set an attribute, pass in the new value.

	Methods:
	--------
	id
	type
	observed
	seq_5
	seq_3
	ncbi_build
	ncbi_chr_hits
	ncbi_ctg_hits
	ncbi_seq_loc
	ucsc_build
	ucsc_chr_hits
	ucsc_ctg_hits
	heterozygous
	heterozygous_SE
	validated
	genotype
	handle
	batch_id
	method
	locus_id
	symbol
	mrna
	protein
	functional_class

   is_subsnp
	Title	: is_subsnp
	Usage	: $is = $snp->is_subsnp()
	Function: returns 1 if $snp is a subSNP
	Returns : 1 or undef
	Args	: NONE

   subsnp
	Title	: subsnp
	Usage	: $subsnp = $snp->subsnp()
	Function: returns the currently active subSNP of $snp
	Returns : Bio::Variation::SNP
	Args	: NONE

   add_subsnp
	Title	: add_subsnp
	Usage	: $subsnp = $snp->add_subsnp()
	Function: pushes the previous value returned by subsnp() onto a stack,
		  accessible with each_subsnp().
		  Sets return value of subsnp() to a new Bio::Variation::SNP
		  object, and returns that object.
	Returns : Bio::Varitiation::SNP
	Args	: NONE

   each_subsnp
	Title	: each_subsnp
	Usage	: @subsnps = $snp->each_subsnp()
	Function: returns a list of the subSNPs of a refSNP
	Returns : list
	Args	: NONE

perl v5.14.2							    2012-03-02						  Bio::Variation::SNP(3pm)
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