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Full Discussion: Pattern matching using awk from a file
Top Forums UNIX for Beginners Questions & Answers Pattern matching using awk from a file Post 303045531 by Sanchari on Monday 30th of March 2020 07:28:41 PM
Old 03-30-2020
Pattern matching using awk from a file
Hello, I have a very large file (DB_file.txt) with coordinate positions, example:


example for the DB_file.txt
Code:
chr1    1000    2000    chr1    10000    11000    3    281    0    0.459585414218248    0    0    0    1218    1    1.88650643678468    0    0    0    0.000000425582664277006    3.87833663319237    0.000000425597761316606    0.201115300038799    0.743522481235195    0.822936566866982
chr1    1000    2000    chr1    11000    12000    4    281    0    0.459585414218248    0    0    0    459    1    0.710924839477969    0    0    0    0.000000355375953311341    1.75327208538672    0.000000192399150742434    0.068194541602096    0.101318817290739    0.81707019750747
chr1    1000    2000    chr1    12000    13000    5    281    0    0.459585414218248    0    0    0    1415    1    2.19163104109222    0    0    0    0.000000310867653966458    3.44281554060217    0.000000377804900731428    0.128881860609444    0.263803805858084    0.81707019750747
chr1    1000    2000    chr1    13000    14000    1    281    0    0.459585414218248    0    0    0    437    1    0.676850010570529    0    0    0    0.000000285200375223444    1.49690344452761    0.000000164265976667856    0.335040184988013    0.776177861586765    0.837324774202159
chr1    1000    2000    chr1    14000    15000    1    281    0    0.459585414218248    0    0    0    530    1    0.820893605497437    0    0    0    0.000000271516726063383    1.60662404023105    0.000000176306406449545    0.322230259464951    0.799436461434159    0.850447555722604
chr1    1000    2000    chr1    16000    17000    1    281    0    0.459585414218248    0    0    0    490    1    0.758939371120272    0    0    0    0.000000253854147173018    1.41695624386548    0.000000155492795574155    0.343542270137564    0.75754917047966    0.828368055880824
 chr1    1000    2000   chr1    18000    19000    2    281    0    0.459585414218248    0    0    0    130    1    0.201351261725787    0    0    0    0.000000231422263301451    0.691389012939271    0.0000000758710869983566    0.119714987783608    0.152817308925748    0.81707019750747

I have a pattern file with the following:


Code:
chr1    1000    2000    chr1    10000    11000
chr1    1000    2000    chr1    11000    12000
chr1    1000    2000    chr1    12000    13000

For a single query, I am using the command:
Code:
awk '{if ($1 == "chr1" && $2 == "1000" && $3 == "2000" && $4 == "chr1" && $5 == "38000" && $6 == "39000") print $0}'  DB_file.txt

How can I do for all the patterns in a file ?
 

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LEARN ABOUT DEBIAN

bio::graphics::glyph::wiggle_box

Bio::Graphics::Glyph::wiggle_box(3pm)			User Contributed Perl Documentation		     Bio::Graphics::Glyph::wiggle_box(3pm)

NAME

       Bio::Graphics::Glyph::wiggle_box - A generic box glyph compatible with dense "wig"data

SYNOPSIS

	 See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.

DESCRIPTION

       This glyph works like the regular 'box' glyph but takes value data in Bio::Graphics::Wiggle file format:

	reference = chr1
	ChipCHIP Feature1 1..10000 wigfile=./test.wig;wigstart=0
	ChipCHIP Feature2 10001..20000 wigfile=./test.wig;wigstart=656
	ChipCHIP Feature3 25001..35000 wigfile=./test.wig;wigstart=1312

       The "wigfile" attribute gives a relative or absolute pathname to a Bio::Graphics::Wiggle format file. The optional "wigstart" option gives
       the offset to the start of the data. If not specified, a linear search will be used to find the data. The data consist of a packed binary
       representation of the values in the feature, using a constant step such as present in tiling array data.

       This glyph is intended for dense, qualitative feature data.  Any score data for each data point is only evaluated for true/false, when
       true, a box of the specified bgcolor is drawn, when false, nothing is drawn.  No data smoothing is used.

       Two primary benefits of using this glyph (with wiggle data) are:

	1) For large, genome-wide data sets, the speed of panel rendering is
	   greatly improved.
	2) Large sets of related features can be rendered as a UCSC-style subtrack
	   without the need for  aggregation or a GFF3 containment hierarchy.

       A disadvantage to this approach is that individual features will have no attributes associated with them and will appear as anonymous
       blocks within a sub-track.

       An example use for this glyph is annotated transcribed regions from microarray experiments.  Such regions are identified based on raw
       microarray data but do not necessarily have a score associated with them.  In this case, using the wiggle_box glyph provides a graphical
       summary of an expression array experiment.

   DATA
       The wiggle data used for this glyph should be loaded using the 'BED' format in order to allow features of variable width.  The fourth
       column should be a true value, with numeric or ".".  An example is shown below:

	track type=wiggle_0 name="transfrags" description="D. melanogaster transcribed fragments 0-2hrs"
	2L	9309	9451	1
	2L	10697	11021	1
	2L	11101	11345	1
	2L	11410	11521	1
	2L	11771	12243	1
	2L	12314	12954	1
	2L	13516	15746	1
	2L	17033	17191	1
	2L	18232	18580	1
	2L	19860	19999	1

   OPTIONS
       This glyph accepts the standard generic option set.  It differs in that the label and description and title/mouseover labels apply to the
       whole, panel-wide sub-track feature rather than to individual boxes.

       See Bio::Graphics::Glyph::wiggle_xyplot for a description of the wiggle-specific options and data formats.

BUGS

       Please report them.

SEE ALSO

       Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
       Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
       Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
       Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
       Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
       Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::allele_tower,
       Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

AUTHOR

       Sheldon McKay  <mckays@cshl.edu>.

       Copyright (c) 2008 Cold Spring Harbor Laboratory

       This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either
       version 1, or at your option, any later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text. In addition,
       please see DISCLAIMER.txt for disclaimers of warranty.

perl v5.14.2							    2012-02-20				     Bio::Graphics::Glyph::wiggle_box(3pm)
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