awk code to reconstruct sequence from alignment Post: 302835927

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Top Forums UNIX for Dummies Questions & Answers awk code to reconstruct sequence from alignment Post 302835927 by Fahmida on Tuesday 23rd of July 2013 09:09:40 AM

07-23-2013

Registered User

Dear Yoda,

Thanks for your reply. Your code is working, it adds the 'NNNN's after each subject line, it would be great if code is modified to add 'NNNN's at the end of the Sbjct of a whole block (each block starts with 'Score =...' and may contain many Sbjct lines).
For example there are three segments below. If we look at the starting point of 'Sbjcts' at each segment: 11561582, 3294707, 11140709,.

Code:

Score =  139 bits (70), Expect = 7e-30
 Identities = 103/114 (90%)
 Strand = Plus / Plus
Query: 2040     atctagagtattatggtctttttacatattaaatgaaacattttgatcattttcctactt 2099
                |||||| |||||| |||| |||||| ||||||||||||||||||| |||||||||| |||
Sbjct: 11561582 atctagggtattagggtccttttacctattaaatgaaacattttggtcattttcctcctt 11561641
                                                                     
Query: 2100     gtggtatatttttgtgatcaaaatttgaaaatagtatatttaggagaattgccc 2153
                ||||| |||||||||||||||||  ||||||| || ||||||||||||||||||
Sbjct: 11561642 gtggtctatttttgtgatcaaaacatgaaaatggtctatttaggagaattgccc 11561695

Score =  139 bits (70), Expect = 7e-30
 Identities = 103/114 (90%)
 Strand = Plus / Minus
                                                                         
Query: 2040    atctagagtattatggtctttttacatattaaatgaaacattttgatcattttcctactt 2099
               |||||| |||||| |||| |||||| ||||||||||||||||||| ||||||| || || 
Sbjct: 3294707 atctagggtattagggtcattttacctattaaatgaaacattttggtcatttttctcctc 3294648
                                                                
Query: 2100    gtggtatatttttgtgatcaaaatttgaaaatagtatatttaggagaattgccc 2153
               ||||||||||||||||||||||| |||||||| || ||||||||||||||||||
Sbjct: 3294647 gtggtatatttttgtgatcaaaacttgaaaattgtctatttaggagaattgccc 3294594

 Score =  139 bits (70), Expect = 7e-30
 Identities = 103/114 (90%)
 Strand = Plus / Minus
                                                                       
Query: 2040     atctagagtattatggtctttttacatattaaatgaaacattttgatcattttcctactt 2099
                |||||| |||||| | ||||||||  ||||||||||||||||||| |||||||||| |||
Sbjct: 11140709 atctagggtattaggatctttttagctattaaatgaaacattttggtcattttcctcctt 11140650
                                                                  
Query: 2100     gtggtatatttttgtgatcaaaatttgaaaatagtatatttaggagaattgccc 2153
                ||||| ||||||||||| ||||| || |||||||||||||||||||||||||||
Sbjct: 11140649 gtggtttatttttgtgaccaaaacttaaaaatagtatatttaggagaattgccc 11140596

So,
1) Sort the Sbjct based on their starting points in each block i.e 3294707, 11140709, 11561582,
2) Add Sbjcts strings of each block in the order of (1) separated by 'NNNN'.

Expected Output is:

Code:

gtggtatatttttgtgatcaaaacttgaaaattgtctatttaggagaattgccc
atctagggtattagggtcattttacctattaaatgaaacattttggtcatttttctcctcNNNN
gtggtttatttttgtgaccaaaacttaaaaatagtatatttaggagaattgcccatctagggta
ttaggatctttttagctattaaatgaaacattttggtcattttcctccttNNNNatctagggtatt
agggtccttttacctattaaatgaaacattttggtcattttcctccttgtggtctatttttgtgatca
aaacatgaaaatggtctatttaggagaattgccc

Fahmida

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search::gin::query::set

Search::GIN::Query::Set(3pm)				User Contributed Perl Documentation			      Search::GIN::Query::Set(3pm)

NAME

       Search::GIN::Query::Set - Create queries with set operations

VERSION

       version 0.08

SYNOPSIS

	   # build a query like:
	   # (type:pdf OR type:png) AND (name:Homer OR name:Bart)

	   use Search::GIN::Query::Set;
	   use Search::GIN::Query::Manual;

	   my $query = Search::GIN::Query::Set->new(
	       operation => 'INTERSECT',
	       subqueries => [
		   Search::GIN::Query::Manual->new(
		       values => {
			  type => [qw(pdf png)]
		       }
		   ),
		   Search::GIN::Query::Manual->new(
		       values => {
			  name => [qw(Homer Bart)]
		       }
		   ),
	       ]
	   );

DESCRIPTION

       Creates a manual GIN query that can be used to search using basic set theory, in order to build more complex queries.

       This query doesn't provide any specific search, it's just a set operator for subqueries. You can build complex queries by using other set
       queries as subqueries for a set query.

METHODS
/SUBROUTINES
   new
       Creates a new query.

ATTRIBUTES

   subqueries
       The subqueries to process

   operation
       One of the basic set operators: "UNION", "INTERSECT" and "EXCEPT". The default is "UNION"

AUTHOR

       Yuval Kogman <nothingmuch@cpan.org>

COPYRIGHT AND LICENSE

       This software is copyright (c) 2010 by Yuval Kogman, Infinity Interactive.

       This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.

perl v5.10.1							    2011-01-31					      Search::GIN::Query::Set(3pm)

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