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Full Discussion: awk to average target and gene
Top Forums Shell Programming and Scripting awk to average target and gene Post 302951011 by MadeInGermany on Friday 31st of July 2015 07:07:43 AM
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

 

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LEARN ABOUT DEBIAN

bio::updateableseqi

Bio::UpdateableSeqI(3pm)				User Contributed Perl Documentation				  Bio::UpdateableSeqI(3pm)

NAME

       Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates

SYNOPSIS

       See Bio::SeqI for most of the documentation.  See the documentation of the methods for further details.

DESCRIPTION

       Bio::UpdateableSeqI is an interface for Sequence objects which are expected to allow users to perform basic editing functions
       (update/delete) on their component SeqFeatures.

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

   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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - David Block
       Email dblock@gene.pbi.nrc.ca

CONTRIBUTORS

       Ewan Birney forced me to this...

APPENDIX

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

   delete_feature
	Title	: delete_feature
	Usage	: my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
	Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
		  or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent.  Keeps track of the features
		  of the $gene object that may be left as orphans and returns them as a listref.
	Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
		  This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
		  my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
		  $orphanlist is a reference to a list containing $exon{'2'};
	Returns : a listref of orphaned features after the deletion of $feature (optional)
	Args	: $feature - the feature to be deleted
		  $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
				transcripts in a gene.
		  $gene - the gene containing the $transcript and/or the $feature

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