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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 MOJAVE

test::script

Test::Script(3) 					User Contributed Perl Documentation					   Test::Script(3)

NAME

       Test::Script - Basic cross-platform tests for scripts

DESCRIPTION

       The intent of this module is to provide a series of basic tests for 80% of the testing you will need to do for scripts in the script (or
       bin as is also commonly used) paths of your Perl distribution.

       Further, it aims to provide this functionality with perfect platform-compatibility, and in a way that is as unobtrusive as possible.

       That is, if the program works on a platform, then Test::Script should always work on that platform as well. Anything less than 100% is
       considered unacceptable.

       In doing so, it is hoped that Test::Script can become a module that you can safely make a dependency of all your modules, without risking
       that your module won't on some platform because of the dependency.

       Where a clash exists between wanting more functionality and maintaining platform safety, this module will err on the side of platform
       safety.

FUNCTIONS

   script_compiles
	   script_compiles( 'script/foo.pl', 'Main script compiles' );

       The "script_compiles" test calls the script with "perl -c script.pl", and checks that it returns without error.

       The path it should be passed is a relative unix-format script name. This will be localised when running "perl -c" and if the test fails the
       local name used will be shown in the diagnostic output.

       Note also that the test will be run with the same perl interpreter that is running the test script (and not with the default system perl).
       This will also be shown in the diagnostic output on failure.

   script_runs
	   script_runs( 'script/foo.pl', 'Main script runs' );

       The "script_runs" test executes the script with "perl script.pl" and checks that it returns success.

       The path it should be passed is a relative unix-format script name. This will be localised when running "perl -c" and if the test fails the
       local name used will be shown in the diagnostic output.

       The test will be run with the same perl interpreter that is running the test script (and not with the default system perl). This will also
       be shown in the diagnostic output on failure.

SUPPORT

       All bugs should be filed via the bug tracker at

       <http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Test-Script>

       For other issues, or commercial enhancement and support, contact the author.

AUTHOR

       Adam Kennedy <adamk@cpan.org>

SEE ALSO

       prove, <http://ali.as/>

COPYRIGHT

       Copyright 2006 - 2009 Adam Kennedy.

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

       The full text of the license can be found in the LICENSE file included with this module.

perl v5.18.2							    2009-11-23							   Test::Script(3)
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