Building intervals Post: 302904417

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Top Forums UNIX for Dummies Questions & Answers Building intervals Post 302904417 by lsantome on Wednesday 4th of June 2014 04:45:01 AM

06-04-2014

Registered User

Building intervals

Hi all,

I hope you can help me with the following question:

I have multiple tables like this:

Code:

      Chr    Start    End    Zygosity    Gene
chr1    153233510    153233510    het    LOR
chr1    153233615    153233615    hom    LOR
chr1    153233701    153233701    hom    LOR
chr1    153233728    153233728    hom    LOR
chr1    153233734    153233734    hom    LOR
chr1    153234295    153234295    het    LOR
chr1    153234602    153234602    hom    LOR
chr1    155205331    155205331    hom    GBA
chr1    155205669    155205669    hom    GBA
chr1    155208647    155208647    het    GBA
chr1    155208647    155208647    hom    GBA
chr1    155209338    155209341    het    GBA
chr1    155209341    155209341    hom    GBA
chr1    155209360    155209360    het    GBA
chr1    155214473    155214473    hom    GBA
chr2    159831015    159831015    hom    TANC1
chr2    128018063    128018063    het    ERCC3
chr2    128018192    128018192    hom    ERCC3
chr2    128018916    128018917    hom    ERCC3
chr2    128018919    128018919    hom    ERCC3
chr2    128018920    128018920    hom    ERCC3
chr2    128018926    128018927    het    ERCC3
chr2    128018928    128018928    het    ERCC3
chr2    128018930    128018930    het    ERCC3
chr2    128019178    128019178    hom    ERCC3
chr2    128047101    128047101    hom    ERCC3
chr2    128048142    128048142    hom    ERCC3
chr2    128050134    128050134    hom    ERCC3

What I need to do is to find, for every group in the "Gene" column, correlative lines where "Zygosity"=hom (there must be more than one per group). Once it's done, the interval is defined by the "Chr" value, "Start" value of the first element and the "End" value of the last element.

The expected output for the example above should be:

Code:

      Chr   Start   End   Gene   Width 
chr1 153233615   153233734   LOR   119       
chr1   153234602   155205669   GBA   1971067 
      chr2   128018192   128018920   ERCC3   728 
      chr2   128019178   128050134   ERCC3   30956

I'm not asking for a complete solution but a hint to start. All suggestions are welcome.

Thamks!

Last edited by Franklin52; 06-04-2014 at 05:52 AM.. Reason: Please use code tags

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html::formattext

HTML::FormatText(3)					User Contributed Perl Documentation				       HTML::FormatText(3)

NAME

       HTML::FormatText - Format HTML as plaintext

SYNOPSIS

	require HTML::TreeBuilder;
	$tree = HTML::TreeBuilder->new->parse_file("test.html");

	require HTML::FormatText;
	$formatter = HTML::FormatText->new(leftmargin => 0, rightmargin => 50);
	print $formatter->format($tree);

DESCRIPTION

       The HTML::FormatText is a formatter that outputs plain latin1 text.  All character attributes (bold/italic/underline) are ignored.
       Formatting of HTML tables and forms is not implemented.

       You might specify the following parameters when constructing the formatter:

       leftmargin (alias lm)
	   The column of the left margin. The default is 3.

       rightmargin (alias rm)
	   The column of the right margin. The default is 72.

SEE ALSO

       HTML::Formatter

COPYRIGHT

       Copyright (c) 1995-2002 Gisle Aas, and 2002- Sean M. Burke. All rights reserved.

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

       This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of
       merchantability or fitness for a particular purpose.

AUTHOR

       Current maintainer: Sean M. Burke <sburke@cpan.org>

       Original author: Gisle Aas <gisle@aas.no>

perl v5.12.1							    2004-06-02						       HTML::FormatText(3)