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Full Discussion: Perl to parse a variety of formats
Top Forums Shell Programming and Scripting Perl to parse a variety of formats Post 302996746 by Aia on Tuesday 2nd of May 2017 12:14:33 AM
Old 05-02-2017
While in Perl you could execute a lot of code at the command line, I would recommend that you use one-liners and executable for just testing concepts and quick throw-away.

For example, I want to test that I can split the line by tabs and work with the second field.
I want to extract information from the second field. I might do the following:

Code:
cat example.txt
Input Variant    Errors    Chromosomal Variant    Coding Variant(s)
NM_004992.3:c.274G>T        NC_000023.10:g.153297761C>A    XM_005274683.1:c.-6G>T    XM_005274682.1:c.-6G>T    XM_005274681.1:c.274G>T    LRG_764t2:c.274G>T    NM_004992.3:c.274G>T    LRG_764t1:c.310G>T    NM_001110792.1:c.310G>
NM_004992.3:c.274G>T        NC_0000X.10:g.153297761C>A    XM_005274683.1:c.-6G>T    XM_005274682.1:c.-6G>T    XM_005274681.1:c.274G>T    LRG_764t2:c.274G>T    NM_004992.3:c.274G>T    LRG_764t1:c.310G>T    NM_001110792.1:c.310G>T

Code:
perl -nale '@f = $F[1] =~ /NC_0+(\w+)\.\d+:g\.(\d+)(\w)>(\w)/; print join "\t", @f[0,1],$f[1],@f[2,3]' example.txt

23      153297761       153297761       C       A
X       153297761       153297761       C       A

Now, that I know that my regex is extracting what I want, let's implement it to keep:
Code:
#!/usr/bin/perl
# extract.pl
use strict;
use warnings;

{
    local $, = "\t";
    while(<>) {
        my @fields = split /\t+/;
        my @u = $fields[1] =~ /NC_0+(\w+)\.\d+:g\.(\d+)(\w)>(\w)/;
        print @u[0,1],$u[1],@u[2,3] . "\n" if @u;
    }
}


Code:
perl extract.pl example.txt
23      153297761       153297761       C       A
X       153297761       153297761       C       A

Last edited by Aia; 05-02-2017 at 01:47 AM.. Reason: remove scalar
This User Gave Thanks to Aia For This Post:
cmccabe
 

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LEARN ABOUT DEBIAN

locale::currency

Locale::Currency(3perl) 				 Perl Programmers Reference Guide				   Locale::Currency(3perl)

NAME

       Locale::Currency - standard codes for currency identification

SYNOPSIS

	   use Locale::Currency;

	   $curr = code2currency('usd');     # $curr gets 'US Dollar'
	   $code = currency2code('Euro');    # $code gets 'eur'

	   @codes   = all_currency_codes();
	   @names   = all_currency_names();

DESCRIPTION

       The "Locale::Currency" module provides access to standard codes used for identifying currencies and funds, such as those defined in ISO
       4217.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 4217
       three-letter codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying currencies. The ones currently supported are:

       alpha
	   This is a set of three-letter (uppercase) codes from ISO 4217 such as EUR for Euro.

	   Two of the codes specified by the standard (XTS which is reserved for testing purposes and XXX which is for transactions where no
	   currency is involved) are omitted.

	   This code set is identified with the symbol "LOCALE_CURR_ALPHA".

	   This is the default code set.

       num This is the set of three-digit numeric codes from ISO 4217.

	   This code set is identified with the symbol "LOCALE_CURR_NUMERIC".

ROUTINES

       code2currency ( CODE [,CODESET] )
       currency2code ( NAME [,CODESET] )
       currency_code2code ( CODE ,CODESET ,CODESET2 )
       all_currency_codes ( [CODESET] )
       all_currency_names ( [CODESET] )
       Locale::Currency::rename_currency  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Currency::add_currency  ( CODE ,NAME [,CODESET] )
       Locale::Currency::delete_currency  ( CODE [,CODESET] )
       Locale::Currency::add_currency_alias  ( NAME ,NEW_NAME )
       Locale::Currency::delete_currency_alias	( NAME )
       Locale::Currency::rename_currency_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Currency::add_currency_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Currency::delete_currency_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes man page.

SEE ALSO

       Locale::Codes
       Locale::Constants
       http://www.iso.org/iso/support/currency_codes_list-1.htm
	   The ISO 4217 data.

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 1997-2001 Canon Research Centre Europe (CRE).
	  Copyright (c) 2001	  Michael Hennecke
	  Copyright (c) 2001-2010 Neil Bowers
	  Copyright (c) 2010-2011 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.14.2							    2011-09-26						   Locale::Currency(3perl)
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