Outputting characters after a given string and reporting the characters in the row below --sed Post: 303028771

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Top Forums Shell Programming and Scripting Outputting characters after a given string and reporting the characters in the row below --sed Post 303028771 by Xterra on Monday 14th of January 2019 02:55:22 PM

01-14-2019

Registered User

Don
I modified a bit your script to output the total count and give some format:

Code:

awk -v gene="gene-a gene-b" -v lengths="3 6" -v strings="GCATGAAAACATACA TTTCCAGAAATTGT" '
BEGIN {	nString = split(strings, String)
	split(lengths, OutLen)
	split(gene, Id)
	for(i = 1; i <= nString; i++)
		StringLen[i] = length(String[i])
}
/^@/ {	getline CodonLine
	getline
	getline QualityLine
	for(i = 1; i <= nString; i++)
		if(spot = index(CodonLine, String[i]))
			printf("Gene:\t"Id[i]"\tCodon:\t%s\t\tQuality Score:\t%s\t\n",
			    substr(CodonLine, spot + StringLen[i], OutLen[i]),
			    substr(QualityLine, spot + StringLen[i], OutLen[i]))
}' test.txt | awk '{ count[$0]++ } END {{ print "\n\t\t\t\tSummary\n#############################################################################\nCount\t\tGene\t\tCodon\t\t\tQuality Score\n" } {for (gene in count ) print count[gene] "\t" gene | "sort -k 3"}}'

With the above script I am getting the desired output:

Code:

                                Summary
#############################################################################
Count           Gene            Codon                   Quality Score

1       Gene:   gene-a  Codon:  AAC             Quality Score:  ,ED
2       Gene:   gene-a  Codon:  AAC             Quality Score:  GCC
1       Gene:   gene-a  Codon:  TTT             Quality Score:  +GG
2       Gene:   gene-b  Codon:  TCCAAG          Quality Score:  DGGCGG
1       Gene:   gene-b  Codon:  TCCAAG          Quality Score:  G7DCGG

However, I tried to include the END step in your awk script fail miserably. How can I modify the script so I don't have to "stitch" together the two scripts as shown above?
Thanks!

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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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