NAME
BioUtil::Util - Utilities for operation on data or file
Some great modules like BioPerl provide many robust solutions. However, it is not easy to install for someone in some platforms. And for some simple task scripts, a lite module may be a good choice. So I reinvented some wheels and added some useful utilities into this module, hoping it would be helpful.
VERSION
Version 2014.1115
EXPORT
file_list_from_argv
get_file_list
extract_parameters_from_string
get_parameters_from_file
get_list_from_file
get_column_data
read_json_file
write_json_file
run
check_positive_integer
filename_prefix
check_all_files_exist
check_in_out_dir
rm_and_mkdirSYNOPSIS
use BioUtil::Util;SUBROUTINES/METHODS
file_list_from_argv
Get file list from @ARGV. You should use this after parsing options!
When no arguments given, 'STDIN' will be added to the list, which could be further used by, e.g. FastaReader.
get_file_list
Find files/directories with custom filter, max serach depth could be specified.
Example (searching perl scripts)
my $dir = "~";
my $depth = 2;
my $list = get_file_list(
$dir,
sub {
if ( -d or /^\./i ) { # ignore configuration file and folders
return 0;
}
if (/\.pm/i or /\.pl/i) {
return 1;
}
return 0;
},
$depth
);
print "$_\n" for @$list;extract_parameters_from_string
Extract parameters from string.
The regular expression is
/([\w\d\_\-\.]+)\s*=\s*([^\=;]*)[\s;]*/Example:
# bad format, but could also be parsed
# my $s = " s = b; a=test; b_c=12 3; a.b =; b
# = asdf
# sd; ads-f = 12313";
# recommended
my $s = "key1=abcde; key2=123; conf.a=file; conf.b=12; ";
my $pa = extract_parameters_from_string($s);
print "=$_:$$p{$_}=\n" for sort keys %$pa;get_parameters_from_file
Get parameters from a file. Comments start with # are allowed in file.
Example:
my $pa = get_parameters_from_file("d.txt");
print "$_: $$pa{$_}\n" for sort keys %$pa;For a file with content:
# cell phone
apple = 1 # note
nokia = 2 #output is:
apple: 1
nokia: 2get_list_from_file
Get list from a file. Comments start with # are allowed in file.
Example:
my $list = get_list_from_file("d.txt");
print "$_\n" for @$list;For a file with content:
# cell phone
apple # note
nokiaoutput is:
apple
nokiaget_column_data
Get one column of a file.
Example:
my $list = get_column_data("d.txt", 2);
print "$_\n" for @$list;read_json_file
Read json file and decode it into a hash ref.
Example:
my $hashref = read_json_file($file);write_json_file
Write a hash ref into a file.
Example:
my $hashref = { "a" => 1, "b" => 2 };
write_json_file($hashref, $file);run
Run a command
Example:
run('date');check_positive_integer
Check Positive Integer
Example:
rcheck_positive_integer(1);check_positive_integer
Get filename prefix
Example:
filename_prefix("test.fa"); # "test"
filename_prefix("tmp"); # "tmp"check_all_files_exist
Check whether all files existed.check_in_out_dir
Check in and out directory.Example:
check_in_out_dir("~/dir", "~/dir.out");rm_and_mkdir
Make a directory, remove it firstly if it exists.Example:
rm_and_mkdir("out")