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Top Forums Shell Programming and Scripting awk to parse section of csv into array Post 303032144 by cmccabe on Tuesday 12th of March 2019 08:27:49 PM
Old 03-12-2019
awk to parse section of csv into array

In the awk below I am trying to parse the Sample Name below the [Data] section. The values that are extracted are read into array s(each value in a row seperated by a space) which will be used later in a bash script. The awk does execute but no values are printed. I am also not sure how to print in a row each value seperated by a space.
Maybe pipe the output to paste -s -d, - to put a space in-place of a comma in k? Thank you Smilie.

awk
Code:
s=$(awk -F'.' -v section="[Data]" -v k="Sample Name"  '  
$0==section{ f=1; next }  ## flag when section is found in file
/\[/{ f=0; next }        ## # For any lines with [ disable the flag     
f && $2==k{ print $0 })' file.csv  ## # If flag is set and first field is the key print k=value

file.csv
Code:
[Settings]		
Adapter	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA	
AdapterRead2	AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT	
		
[Data]		
Sample_ID	Sample_Name	Sample_Plate
Sample_1	19-0000-Last-First	
Sample_2	19-0001-La-Fi	
Sample_3	19-0003-L-F	
Sample_4	19-0004-Las-Fir

desired output ---- contents of s ----
Code:
19-0000-Last-First 19-0001-La-Fi 19-0003-L-F 19-0004-Las-Fir

 

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CSV(3pm)						User Contributed Perl Documentation						  CSV(3pm)

NAME
Class::CSV - Class based CSV parser/writer SYNOPSIS
use Class::CSV; my $csv = Class::CSV->parse( filename => 'test.csv', fields => [qw/item qty sub_total/] ); foreach my $line (@{$csv->lines()}) { $line->sub_total('$'. sprintf("%0.2f", $line->sub_total())); print 'Item: '. $line->item(). " ". 'Qty: '. $line->qty(). " ". 'SubTotal: '. $line->sub_total(). " "; } my $cvs_as_string = $csv->string(); $csv->print(); my $csv = Class::CSV->new( fields => [qw/userid username/], line_separator => " "; ); $csv->add_line([2063, 'testuser']); $csv->add_line({ userid => 2064, username => 'testuser2' }); DESCRIPTION
This module can be used to create objects from CSV files, or to create CSV files from objects. Text::CSV_XS is used for parsing and creating CSV file lines, so any limitations in Text::CSV_XS will of course be inherant in this module. EXPORT None by default. METHOD
CONSTRUCTOR parse the parse constructor takes a hash as its paramater, the various options that can be in this hash are detailed below. Required Options o fields - an array ref containing the list of field names to use for each row. there are some reserved words that cannot be used as field names, there is no checking done for this at the moment but it is something to be aware of. the reserved field names are as follows: "string", "set", "get". also field names cannot contain whitespace or any characters that would not be allowed in a method name. Source Options (only one of these is needed) o filename - the path of the CSV file to be opened and parsed. o filehandle - the file handle of the CSV file to be parsed. o objects - an array ref of objects (e.g. Class::DBI objects). for this to work properly the field names provided in fields needs to correspond to the field names of the objects in the array ref. o classdbi_objects - depreciated use objects instead - using classdbi_objects will still work but its advisable to update your code. Optional Options o line_separator - the line seperator to be included at the end of every line. defaulting to " " (unix carriage return). new the new constructor takes a hash as its paramater, the same options detailed in parse apply to new however no Source Options can be used. this constructor creates a blank CSV object of which lines can be added via add_line. ACCESSING lines returns an array ref containing objects of each CSV line (made via Class::Accessor). the field names given upon construction are available as accessors and can be set or get. for more information please see the notes below or the perldoc for Class::Accessor. the lines accessor is also able to be updated/retrieved in the same way as individual lines fields (examples below). Example retrieving the lines: my @lines = @{$csv->lines()}; removing the first line: pop @lines; $csv->lines(@lines); sorting the lines: @lines = sort { $a->userid() <=> $b->userid() } @lines: $csv->lines(@lines); sorting the lines (all-in-one way): $csv->lines([ sort { $a->userid() <=> $b->userid() } @{$csv->lines()} ]); Retrieving a fields value there is two ways to retrieve a fields value (as documented in Class::Accessor). firstly you can call the field name on the object and secondly you can call "get" on the object with the field name as the argument (multiple field names can be specified to retrieve an array of values). examples are below. my $value = $line->test(); OR my $value = $line->get('test'); OR my @values = $line->get(qw/test test2 test3/); Setting a fields value setting a fields value is simmilar to getting a fields value. there are two ways to set a fields value (as documented in Class::Accessor). firstly you can simply call the field name on the object with the value as the argument or secondly you can call "set" on the object with a hash of fields and their values to set (this isn't standard in Class::Accessor, i have overloaded the "set" method to allow this). examples are below. $line->test('123'); OR $line->set( test => '123' ); OR $line->set( test => '123', test2 => '456' ); Retrieving a line as a string to retrieve a line as a string simply call "string" on the object. my $string = $line->string(); new_line returns a new line object, this can be useful for to "splice" a line into lines (see example below). you can pass the values of the line as an ARRAY ref or a HASH ref. Example my $line = $csv->new_line({ userid => 123, domainname => 'splicey.com' }); my @lines = $csv->lines(); splice(@lines, 1, 0, $line); OR splice(@{$csv->lines()}, 1, 0, $csv->new_line({ userid => 123, domainname => 'splicey.com' })); add_line adds a line to the lines stack. this is mainly useful when the new constructor is used but can of course be used with any constructor. it will add a new line to the end of the lines stack. you can pass the values of the line as an ARRAY ref or a HASH ref. examples of how to use this are below. Example $csv->add_line(['house', 100000, 4]); $csv->add_line({ item => 'house', cost => 100000, bedrooms => 4 }); OUTPUT string returns the object as a string (CSV file format). print calls "print" on string (prints the CSV to STDOUT). SEE ALSO
Text::CSV_XS, Class::Accessor AUTHOR
David Radunz, <david@boxen.net> COPYRIGHT AND LICENSE
Copyright 2004 by David Radunz This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.10.0 2007-02-08 CSV(3pm)
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