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Full Discussion: Re ordering lines - Awk
Top Forums Shell Programming and Scripting Re ordering lines - Awk Post 302543740 by quincyjones on Tuesday 2nd of August 2011 01:45:02 AM
Old 08-02-2011
Re ordering lines - Awk

Is it possible to re-order certain rows as columns (of large files).
Few lines from the file for reference.

Splicing Factor: Tra2beta, Motif: aaguguu, Cutoff: 0.5000
Sequence Position	Genomic Coordinate	K-mer     	Score   
97               	chr1:67052604     	uacuguu   	0.571   
147              	chr1:67052554     	augugua   	0.536   
166              	chr1:67052535     	aaauuuu   	0.500   
226              	chr1:67052475     	aauugug   	0.612   
Splicing Factor: SRp20, Motif: wcwwc, Cutoff: 0.7200
Sequence Position	Genomic Coordinate	K-mer     	Score   
302              	chr1:67052399     	ucauc     	0.875   
349              	chr1:67052352     	acauc     	0.740

Splicing_Factor	Motif	Cutoff	Sequence_Position	Genomic_Coordinate	K-mer	Score   
Tra2beta	aaguguu	0.5000	97	chr1:67052604     	uacuguu   	0.571
Tra2beta	aaguguu	0.5000	147	chr1:67052554     	augugua   	0.536
Tra2beta	aaguguu	0.5000	166	chr1:67052535     	aaauuuu   	0.500 
Tra2beta	aaguguu	0.5000	226	chr1:67052475     	aauugug   	0.612
SRp20	wcwwc	0.7200	302	chr1:67052399	ucauc	0.875   
SRp20	wcwwc	0.7200	349	chr1:67052352	acauc	0.740

Last edited by quincyjones; 08-02-2011 at 02:52 AM..
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Bio::Graphics::Glyph::wiggle_density(3pm)		User Contributed Perl Documentation		 Bio::Graphics::Glyph::wiggle_density(3pm)

Bio::Graphics::Glyph::wiggle_density - A density plot compatible with dense "wig"data SYNOPSIS
See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>. DESCRIPTION
This glyph works like the regular density 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. OPTIONS The same as the regular graded_segments glyph, except that the following options are recognized: Name Value Description ---- ----- ----------- basedir path Path to be used to resolve "wigfile" and "densefile" tags giving relative paths. Default is to use the current working directory. Absolute wigfile & densefile paths will not be changed. autoscale "local" or "global" If one or more of min_score and max_score options are absent, then these values will be calculated automatically. The "autoscale" option controls how the calculation is done. The "local" value will scale values according to the minimum and maximum values present in the window being graphed. "global" will use chromosome-wide statistics for the entire wiggle or dense file to find min and max values. smoothing method name Smoothing method: one of "mean", "max", "min" or "none" smoothing_window integer Number of values across which data should be smoothed. bicolor_pivot name Where to pivot the two colors when drawing bicolor plots. Options are "mean" and "zero". A numeric value can also be provided. pos_color color When drawing bicolor plots, the fill color to use for values that are above the pivot point. neg_color color When drawing bicolor plots, the fill color to use for values that are below the pivot point. SPECIAL FEATURE TAGS The glyph expects one or more of the following tags (attributes) in feature it renders: Name Value Description ---- ----- ----------- wigfile path name Path to the Bio::Graphics::Wiggle file for vales. (required) densefile path name Path to a Bio::Graphics::DenseFeature object (deprecated) denseoffset integer Integer offset to where the data begins in the Bio::Graphics::DenseFeature file (deprecated) densesize integer Integer size of the data in the Bio::Graphics::DenseFeature file (deprecated) 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
Lincoln Stein <>. Copyright (c) 2007 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_density(3pm)

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