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Full Discussion: Cannot subset ranges from another range set
Top Forums UNIX for Beginners Questions & Answers Cannot subset ranges from another range set Post 303042672 by Scrutinizer on Friday 3rd of January 2020 05:17:23 AM
Old 01-03-2020
You would need to compare $5 and $6 to all the ranges in $2, $3 so you would need to put them in memory first, so a way to do it would be to read the inputfile twice, the first time to put $2, $3 in memory, the second time to compare $5 and $6 to the ranges.

A simple first approach, assuming that $1 is always he same value could look something like this:

Code:
awk '
  NR==FNR {                                                    # When reading the file for the first time
    R[$2 FS $3]                                                # Store the ranges $2 to $3 in array R, using the standard field separator
    next
  }
  {                                                            # When reading the file for the second time
    for(i in R) {                                              # For every line, for every range
      split(i,F)                                               # Split the stored range in minimum and maximum using the standard field separator
      if(F[1]<=$5 && $5<=F[2])                                 # F[1] will contain the minimum, F[2] the maximum, so if $5 , $6 are inside it.
        print $0, "range " $5 "-" $6 " inside " F[1] "-" F[2]  # print the result
    }
  }
' infile infile                                                # read the file twice

With your data this should produce:
Code:
Ca21chr2_C_albicans_SC5314	618550	627903	Ca21chr2_C_albicans_SC5314	7510	8043 range 7510-8043 inside 5286-50509

Last edited by Scrutinizer; 01-03-2020 at 06:31 AM..
This User Gave Thanks to Scrutinizer For This Post:
cryptodice
 

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LEARN ABOUT DEBIAN

ppi::token::quote

PPI::Token::Quote(3pm)					User Contributed Perl Documentation				    PPI::Token::Quote(3pm)

NAME

       PPI::Token::Quote - String quote abstract base class

INHERITANCE

	 PPI::Token::Quote
	 isa PPI::Token
	     isa PPI::Element

DESCRIPTION

       The "PPI::Token::Quote" class is never instantiated, and simply provides a common abstract base class for the four quote classes.  In PPI,
       a "quote" is limited to only the quote-like things that themselves directly represent a string. (although this includes double quotes with
       interpolated elements inside them).

       The subclasses of "PPI::Token::Quote" are:

       '' - PPI::Token::Quote::Single
       "q{}" - PPI::Token::Quote::Literal
       "" - PPI::Token::Quote::Double
       "qq{}" - PPI::Token::Quote::Interpolate

       The names are hopefully obvious enough not to have to explain what each class is here. See their respective pages for more details.

       Please note that although the here-doc does represent a literal string, it is such a nasty piece of work that in PPI it is given the honor
       of its own token class (PPI::Token::HereDoc).

METHODS

   string
       The "string" method is provided by all four ::Quote classes. It won't get you the actual literal Perl value, but it will strip off the
       wrapping of the quotes.

	 # The following all return foo from the ->string method
	 'foo'
	 "foo"
	 q{foo}
	 qq <foo>

   literal
       The "literal" method is provided by ::Quote:Literal and ::Quote::Single.  This returns the value of the string as Perl sees it: without the
       quote marks and with "\" and "'" resolved to "" and "'".

       The "literal" method is not implemented by ::Quote::Double or ::Quote::Interpolate yet.

SUPPORT

       See the support section in the main module.

AUTHOR

       Adam Kennedy <adamk@cpan.org>

COPYRIGHT

       Copyright 2001 - 2011 Adam Kennedy.

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

       The full text of the license can be found in the LICENSE file included with this module.

perl v5.10.1							    2011-02-26						    PPI::Token::Quote(3pm)
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