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Top Forums Shell Programming and Scripting Match ids and print original file Post 302777479 by nans on Friday 8th of March 2013 03:31:23 AM
Old 03-08-2013
Match ids and print original file

Hello,

I have two files

Original: ( 5000 entries)
Chr Position
chr1 879108
chr1 881918
chr1 896874 ...

and a file with allele freq ( 2000 entries)
Chr Position MAF
chr1 881918 0.007
chr1 979748 0.007
chr1 1120377 0.007
chr1 1178925 0.036

I would like the original file matched with the allele freq and print out the output file with 5000 entries.
Chr Position MAF
chr1 879108 NULL
chr1 881918 0.007
chr1 896874 NULL
...

Any help is appreciated. Thank you.

Last edited by nans; 03-08-2013 at 04:59 AM..
 

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

NAME
Bio::Graphics::Glyph::wiggle_xyplot - An xyplot plot compatible with dense "wig"data SYNOPSIS
See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>. DESCRIPTION
This glyph works like the regular xyplot but takes value data in Bio::Graphics::Wiggle file format: reference = chr1 ChipCHIP Feature1 1..10000 wigfile=./test.wig ChipCHIP Feature2 10001..20000 wigfile=./test.wig ChipCHIP Feature3 25001..35000 wigfile=./test.wig The "wigfile" attribute gives a relative or absolute pathname to a Bio::Graphics::Wiggle format file. 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. Wigfiles are created using the Bio::Graphics::Wiggle module or the wiggle2gff3.pl script, currently both part of the gbrowse package. Alternatively, you can place an array of quantitative data directly in the "wigdata" attribute. This can be an arrayref of quantitative data starting at feature start and ending at feature end, or the data string returned by Bio::Graphics::Wiggle->export_to_wif64($start,$end). OPTIONS In addition to all the xyplot glyph options, 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. variance_band boolean If true, draw a grey band across entire plot showing mean and +/- 1 standard deviation (for wig files only). 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 or object for quantitative values. wigdata string Data exported from a Bio::Graphics::Wiggle in WIF format using its export_to_wif64() method. 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 <steinl@cshl.edu>. 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_xyplot(3pm)
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