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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 CENTOS

sieveshell

SIEVESHELL(1)						User Contributed Perl Documentation					     SIEVESHELL(1)

NAME

       sieveshell - remotely manipulate sieve scripts

SYNOPSIS

       sieveshell [--user=user] [--authname=authname] [--realm=realm] [--exec=script] server[:port]

       sieveshell --help

DESCRIPTION

       sieveshell allows users to manipulate their scripts on a remote server.	It works via MANAGESIEVE, a work in progress.

       The following commands are recognized:

	   list list scripts on server.

	   put <filename> upload script to server.

	   get <name> [<filename>] get script. if no filename display to stdout

	   delete <name> delete script.

	   activate <name> activate script.

	   deactivate deactivate all scripts.

OPTIONS

       -u user, --user=user
	   The authorization name to request; by default, derived from the authentication credentials.

       -a authname, --authname=authname
	   The user to use for authentication (defaults to current user).

       -r realm, --realm=realm
	   The realm to attempt authentication in.

       -e script, --exec=script
	   Instead of working interactively, run commands from script, and exit when done.

REFERENCES

       [MANAGESIEVE] Martin, T.; "A Protocol for Remotely Managing Sieve Scripts", draft-ietf-managesieve-03.txt, Mirapoint, Inc.; May 2001, work
       in progress.

AUTHOR

       Tim Martin <tmartin@mirapoint.com>, and the rest of the Cyrus team <cyrus-bugs@andrew.cmu.edu>.

perl v5.16.3							    2014-06-10							     SIEVESHELL(1)
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