10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
What is an efficient way of counting the number of unique values in a 400 column by 1000 row array and outputting the counts per column, assuming the unique values in the array are:
A, B, C, D
In other words the output should look like: Value COL1 COL2 COL3
A 50 51 52... (16 Replies)
Discussion started by: Geneanalyst
16 Replies
2. UNIX for Dummies Questions & Answers
Hi !
input:
A|B|C|D
A|F|C|E
A|B|I|C
A|T|I|B
As the title of the thread says, I would need to get:
1|3|2|4
I tried different variants of this command, but I don't manage to obtain what I need:
gawk 'BEGIN{FS=OFS="|"}{for(i=1; i<=NF; i++) a++} END {for (b in a) print b}' input
... (2 Replies)
Discussion started by: beca123456
2 Replies
3. Shell Programming and Scripting
Hi i have data like
abchd 124 ldskc aattggcc
each separated by tab space i want to count number of characters in 4th column and print it in new column with tabspace for every line can anyone help me how to do it.
Thanks. (3 Replies)
Discussion started by: bhargavpbk88
3 Replies
4. Shell Programming and Scripting
Hi
I was going through the below thread
https://www.unix.com/shell-programming-scripting/48535-how-count-number-fields-record.html
I too have something similar requirement as specified in this thread but the number of columns in my case can be very high, so I am getting following error.
... (3 Replies)
Discussion started by: shekharjchandra
3 Replies
5. Shell Programming and Scripting
This is the source file, we called it errorlist.out
196 server_a server_unix_2 CD
196 server_b server_win_1 CD
196 server_c server_win_2 CD
196 server_bd server_unix_2 CD
196 server_d server_unix_2 CD
196 server_es server_win_1 CD
196 ... (14 Replies)
Discussion started by: sQew
14 Replies
6. UNIX for Dummies Questions & Answers
Could anybody help with this?
I have input below .....
david,39
david,39
emelie,40
clarissa,22
bob,42
bob,42
tim,32
bob,39
david,38
emelie,47
what i want to do is count how many names there are with different ages, so output would be like this ....
david,2
emelie,2
clarissa,1... (3 Replies)
Discussion started by: itsme999
3 Replies
7. Shell Programming and Scripting
im trying to count the number of occurences of column 2 value(starting from KKK*) of the below file, file.txt
using the code cat file.txt | awk ' BEGIN { print "Category Counts"} {FS=","} {NR > 2} { cats = cats + 1} END { for(c in cats) { print c, "=", cats} } '
but its returning as
... (6 Replies)
Discussion started by: michaelrozar17
6 Replies
8. UNIX for Dummies Questions & Answers
Hi All,
I have the following input which i want to process using AWK.
Rows,NC,amount
1,1202,0.192387
2,1201,0.111111
3,1201,0.123456
i want the following output
count of rows = 3 ,sum of amount = 0.426954
Many thanks (2 Replies)
Discussion started by: pistachio
2 Replies
9. Shell Programming and Scripting
Hi,
I am a beginner in awk scripting! I need your help; I want to replace the fifth column number (which is 15 here) here in this file for example :
ATOM 142 N PRO A 15
ATOM 143 CD PRO A 15
ATOM 144 HD1 PRO A 15
ATOM ... (5 Replies)
Discussion started by: adak
5 Replies
10. Shell Programming and Scripting
Hi All,
I have an input below and i would want to do a count on all the term "aaa" and count only once if the number in first column is the same.
For eg, if i use a "grep -c aaa input" command, the count will be "8".
However, i would want the count to be "6" instead since 2 numbers in the 1st... (7 Replies)
Discussion started by: Raynon
7 Replies
Bio::Graphics::Glyph::stackedplot(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::stackedplot(3pm)
NAME
Bio::Graphics::Glyph::stackedplot - The stackedplot glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
The stackedplot glyph can be used to draw quantitative feature data using a stacked column plot. It differs from the xyplot glyph in that
the plot applies to a single top level feature, not a group of subfeatures. The data to be graphed is derived from an attribute called
"data_series."
The data to be graphed is represented as a list of arrays:
(
[1, 2, 8],
[6, 1, 1],
[10,8, 0],
[1, 1, 1],
)
Each array is a column in the stacked plot. Its values become the subdivisions of the column. In this example, there are four columns, each
of which has three subdivisions.
You can add labels to the columns and change the colors of the subdivisions.
To assign data to a feature, you can add a "series" tag:
$snp1 = Bio::SeqFeature::Generic ->new (-start => 500,-end=>501,
-display_name =>'example',
-tag=> { series => [
[10,20,30],
[30,30,0],
[5,45,10],
[5,45,10],
[5,45,10],
[50,0,50],
],
}
);
Note that the series tag must consist of an array of arrays.
If you are using a gff3 representation, you can load a database with data that looks like this:
chr1 test feature 1 1000 . . . series=10 20 30;series=30 30 0;series=5 45 10...
If you are using a gff2 representation, you can load a database with data that looks like this:
chr1 test feature 1 1000 . . . series 10 20 30; series 30 30 0 series 5 45 10...
Or you can pass a callback to the -series option:
$panel->add_track(@data,
-glyph => 'stackedplot',
-series => sub {
my $feature = shift;
return [
[10,20,30],
[30,30,0],
[5,45,10],
]
}
);
OPTIONS
The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
-hilite Highlight color undef (no color)
In addition, the alignment glyph recognizes all the options of the xyplot glyph, as well as the following glyph-specific option:
Option Description Default
------ ----------- -------
-fixed_gap Vertical distance between 8
the rectangle that shows
the start:end range of
the feature and the fixed
width stacked plot.
-series_colors A list giving a series of red,blue,green,orange,
color names for the data brown,grey,black
series (the values inside
each stacked column).
-column_labels A list of labels to print -none-
underneath each column.
-column_width The width of each column. 8
-column_spacing Spacing between each 2
column.
-min_score Minimum score for the 0.0
sum of the members of
each data series.
-max_score Maximum score for the 1.0
sum of the members of each
data series.
-scale_font Font to use for the scale. gdTinyFont
-column_font Font to use for the column gdSmallFont
labels.
-draw_scale Whether to draw a scale to true
right of the columns.
Note that -min_score and -max_score represent the minimum and maximum SUM of all the values in the data series. For example, if your
largest column contains the series (10,20,30), then the -max_score is 60.
EXAMPLE
To understand how this glyph works, try running and modifying the following example:
#!/usr/bin/perl
use strict;
use warnings;
use Bio::Graphics;
use Bio::SeqFeature::Generic;
my $segment = Bio::Graphics::Feature->new(-start=>1,-end=>700);
my $snp1 = Bio::SeqFeature::Generic ->new (-start => 500,-end=>590,
-display_name =>'fred',
-tag=> { series => [
[10,20,30],
[30,30,0],
[5,45,10],
[5,45,10],
[5,45,10],
[50,0,50],
],
},
-source=>'A test',
);
my $snp2 = Bio::SeqFeature::Generic->new(-start => 300,
-end => 301,
-display_name => 'rs12345',
-tag=> {
series => [
[30,20,10 ],
[80,10,10 ],
],
},
-source=>'Another test',
);
my $panel = Bio::Graphics::Panel->new(-segment=>$segment,-width=>800);
$panel->add_track($segment,-glyph=>'arrow',-double=>1,-tick=>2);
$panel->add_track([$snp1,$snp2],
-height => 50,
-glyph => 'stackedplot',
-fixed_gap => 12,
-series_colors => [qw(red blue lavender)],
-column_labels => [qw(a b c d e f g)],
-min_score => 0,
-max_score => 100,
-column_width => 8,
-column_font => 'gdMediumBoldFont',
-scale_font => 'gdTinyFont',
-label => 1,
-description=>1,
);
print $panel->png;
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Track, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::anchored_arrow,
Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::box, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript,
AUTHOR
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2006 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::stackedplot(3pm)