Perl
Perl is a scripting language that excels at text processing.
Contents |
[edit] 1 Library
- BioPerl -- an open source library for Perl bioinformatics coding
[edit] 2 Snippets
[edit] 2.1 Starting a script
Use
#!/usr/bin/env perl
and not
#!/usr/bin/perl
The latter may not work in all environments.
Also make sure to include:
use warnings; use strict;
[edit] 2.2 Trim function
sub trim
{
map { /^\s*(\S.*\S)\s*$/ } @_;
}
[edit] 2.3 Slurp function
This function puts all of a file's contents and returns a string.
sub slurp
{
my $file = shift( @_ );
my $old_terminator = $/;
undef $/;
open( SLURP, $file );
my $slurp = <SLURP>;
close( SLURP );
$/ = $old_terminator;
return $slurp;
}
[edit] 2.4 Change endlines
This will change all Mac and Windows endlines in a file to Unix endlines:
perl -p -i.orig -e 's/\r\n|\r/\n/g' FILENAME
The original file will end up as FILENAME.orig.
[edit] 2.5 Cycle through a directory
opendir( DIR, "$directory_path" ) || die "Cannot open dir $directory_path\n";
while( my $file = readdir( DIR ))
{
//do stuff!
}
close( DIR );
[edit] 3 Resources
- FAS Center: The Scriptome -- Bioinformatics and data oriented Perl scripts put onto the command line for easy use.