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Full Discussion: Awk-Group count of field
Top Forums Shell Programming and Scripting Awk-Group count of field Post 302278286 by patrick chia on Monday 19th of January 2009 11:36:18 PM
Old 01-20-2009
How to use the programming in UNIX to count the total G+C and the GC%?What command li

Seems like can use awk and perl command. But I don't have the idea to write the command line. Thanks for all of your advise.
For example, if I have the file whose content are:
Sample 1. ATAGCAGAGGGAGTGAAGAGGTGGTGGGAGGGAGCT
Sample 2. ACTTTTATTTGAATGTAATATTTGGGACAATTATTC
Sample 3. AAATCATGGTGGGTTTATTGATGGTTAGAAAGTTCC
All the sample above, got 36 nucleotide.

I want my output to count the G + C and GC %. So my output should look like this:
Sample 1: G+C = 21 GC%= 58.33%
Sample 2: G+C = 8 GC%=22.22%
Sample 3: G+C = 13 GC%=36.11%

Thanks and appreciate of your answer.
 

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Spreadsheet::WriteExcel::Chart::Column(3pm)		User Contributed Perl Documentation	       Spreadsheet::WriteExcel::Chart::Column(3pm)

NAME
Column - A writer class for Excel Column charts. SYNOPSIS
To create a simple Excel file with a Column chart using Spreadsheet::WriteExcel: #!/usr/bin/perl -w use strict; use Spreadsheet::WriteExcel; my $workbook = Spreadsheet::WriteExcel->new( 'chart.xls' ); my $worksheet = $workbook->add_worksheet(); my $chart = $workbook->add_chart( type => 'column' ); # Configure the chart. $chart->add_series( categories => '=Sheet1!$A$2:$A$7', values => '=Sheet1!$B$2:$B$7', ); # Add the worksheet data the chart refers to. my $data = [ [ 'Category', 2, 3, 4, 5, 6, 7 ], [ 'Value', 1, 4, 5, 2, 1, 5 ], ]; $worksheet->write( 'A1', $data ); __END__ DESCRIPTION
This module implements Column charts for Spreadsheet::WriteExcel. The chart object is created via the Workbook "add_chart()" method: my $chart = $workbook->add_chart( type => 'column' ); Once the object is created it can be configured via the following methods that are common to all chart classes: $chart->add_series(); $chart->set_x_axis(); $chart->set_y_axis(); $chart->set_title(); These methods are explained in detail in Spreadsheet::WriteExcel::Chart. Class specific methods or settings, if any, are explained below. Column Chart Methods There aren't currently any column chart specific methods. See the TODO section of Spreadsheet::WriteExcel::Chart. EXAMPLE
Here is a complete example that demonstrates most of the available features when creating a chart. #!/usr/bin/perl -w use strict; use Spreadsheet::WriteExcel; my $workbook = Spreadsheet::WriteExcel->new( 'chart_column.xls' ); my $worksheet = $workbook->add_worksheet(); my $bold = $workbook->add_format( bold => 1 ); # Add the worksheet data that the charts will refer to. my $headings = [ 'Number', 'Sample 1', 'Sample 2' ]; my $data = [ [ 2, 3, 4, 5, 6, 7 ], [ 1, 4, 5, 2, 1, 5 ], [ 3, 6, 7, 5, 4, 3 ], ]; $worksheet->write( 'A1', $headings, $bold ); $worksheet->write( 'A2', $data ); # Create a new chart object. In this case an embedded chart. my $chart = $workbook->add_chart( type => 'column', embedded => 1 ); # Configure the first series. (Sample 1) $chart->add_series( name => 'Sample 1', categories => '=Sheet1!$A$2:$A$7', values => '=Sheet1!$B$2:$B$7', ); # Configure the second series. (Sample 2) $chart->add_series( name => 'Sample 2', categories => '=Sheet1!$A$2:$A$7', values => '=Sheet1!$C$2:$C$7', ); # Add a chart title and some axis labels. $chart->set_title ( name => 'Results of sample analysis' ); $chart->set_x_axis( name => 'Test number' ); $chart->set_y_axis( name => 'Sample length (cm)' ); # Insert the chart into the worksheet (with an offset). $worksheet->insert_chart( 'D2', $chart, 25, 10 ); __END__ AUTHOR
John McNamara jmcnamara@cpan.org COPYRIGHT
Copyright MM-MMX, John McNamara. All Rights Reserved. This module is free software. It may be used, redistributed and/or modified under the same terms as Perl itself. perl v5.10.1 2010-02-02 Spreadsheet::WriteExcel::Chart::Column(3pm)
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