NAME

Bio::Root::Utilities - General-purpose utility module

SYNOPSIS

Object Creation

# Using the supplied singleton object:
use Bio::Root::Utilities qw(:obj);
$Util->some_method();

# Create an object manually:
use Bio::Root::Utilities;
my $util = Bio::Root::Utilities->new();
$util->some_method();

$date_stamp = $Util->date_format('yyy-mm-dd');

$clean = $Util->untaint($dirty);

$compressed = $Util->compress('/home/me/myfile.txt')

my ($mean, $stdev) = $Util->mean_stdev( @data );

$Util->authority("me@example.com");
$Util->mail_authority("Something you should know about...");

...and a host of other methods. See below.

DESCRIPTION

Provides general-purpose utilities of potential interest to any Perl script.

The :obj tag is a convenience that imports a $Util symbol into your namespace representing a Bio::Root::Utilities object. This saves you from creating your own Bio::Root::Utilities object via Bio::Root::Utilities->new() or from prefixing all method calls with Bio::Root::Utilities, though feel free to do these things if desired. Since there should normally not be a need for a script to have more than one Bio::Root::Utilities object, this module thus comes with it's own singleton.

INSTALLATION

This module is included with the central Bioperl distribution:

http://www.bioperl.org/wiki/Getting_BioPerl
ftp://bio.perl.org/pub/DIST

Follow the installation instructions included in the README file.

DEPENDENCIES

Inherits from Bio::Root::Root, and uses Bio::Root::IO and Bio::Root::Exception.

Relies on external executables for file compression/uncompression and sending mail. No paths to these are hard coded but are located as needed.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR

Steve Chervitz <sac@bioperl.org>

See the FEEDBACK section for where to send bug reports and comments.

ACKNOWLEDGEMENTS

This module was originally developed under the auspices of the Saccharomyces Genome Database: http://www.yeastgenome.org/

COPYRIGHT

APPENDIX

Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only.

date_format

 Title     : date_format
 Usage     : $Util->date_format( [FMT], [DATE])
 Purpose   : -- Get a string containing the formated date or time
           :    taken when this routine is invoked.
           : -- Provides a way to avoid using `date`.
	   : -- Provides an interface to localtime().
           : -- Interconverts some date formats.
           :
           : (For additional functionality, use Date::Manip or
           :  Date::DateCalc available from CPAN).
 Example   : $Util->date_format();
           : $date = $Util->date_format('yyyy-mmm-dd', '11/22/92');
 Returns   : String (unless 'list' is provided as argument, see below)
           :
           :   'yyyy-mm-dd'  = 1996-05-03    # default format.
           :   'yyyy-dd-mm'  = 1996-03-05
           :   'yyyy-mmm-dd' = 1996-May-03
           :   'd-m-y'       = 3-May-1996
           :   'd m y'       = 3 May 1996
           :   'dmy'         = 3may96
           :   'mdy'         = May 3, 1996
           :   'ymd'         = 96may3
           :   'md'          = may3
           :   'year'        = 1996
           :   'hms'         = 23:01:59  # when not converting a format, 'hms' can be 
           :                             # tacked on to any of the above options
           :                             # to add the time stamp: eg 'dmyhms'
           :   'full' | 'unix' = UNIX-style date: Tue May  5 22:00:00 1998
           :   'list'          = the contents of localtime(time) in an array.
 Argument  : (all are optional)
           : FMT  = yyyy-mm-dd | yyyy-dd-mm | yyyy-mmm-dd |
           :        mdy | ymd | md | d-m-y | hms | hm
           :        ('hms' may be appended to any of these to
	   :        add a time stamp)
           :
           : DATE = String containing date to be converted.
           :        Acceptable input formats:
           :           12/1/97 (for 1 December 1997)
           :           1997-12-01
           :           1997-Dec-01
 Throws    :
 Comments  : If you don't care about formatting or using backticks, you can
           : always use: $date = `date`;
           :
           : For more features, use Date::Manip.pm, (which I should
           : probably switch to...)

month2num

Title      : month2num
Purpose    : Converts a string containing a name of a month to integer
           : representing the number of the month in the year.
Example    : $Util->month2num("march");  # returns 3
Argument   : The string argument must contain at least the first
           : three characters of the month's name. Case insensitive.
Throws     : Exception if the conversion fails.

num2month

Title   : num2month
Purpose : Does the opposite of month2num.
        : Converts a number into a string containing a name of a month.
Example : $Util->num2month(3);  # returns 'Mar'
Throws  : Exception if supplied number is out of range.

compress

Title     : compress
Usage     : $Util->compress(full-path-filename);
          : $Util->compress(<named parameters>);
Purpose   : Compress a file.
Example   : $Util->compress("/usr/people/me/data.txt");
          : $Util->compress(-file=>"/usr/people/me/data.txt",
          :                 -tmp=>1,
          :                 -outfile=>"/usr/people/share/data.txt.gz",
          :                 -exe=>"/usr/local/bin/fancyzip");
Returns   : String containing full, absolute path to compressed file
Argument  : Named parameters (case-insensitive):
          :   -FILE => String (name of file to be compressed, full path).
          :            If the supplied filename ends with '.gz' or '.Z',
          :            that extension will be removed before attempting to compress.
          : Optional:
          :   -TMP  => boolean. If true, (or if user is not the owner of the file)
          :            the file is compressed to a temp file. If false, file may be
          :            clobbered with the compressed version (if using a utility like
          :            gzip, which is the default)
          :   -OUTFILE => String (name of the output compressed file, full path).
          :   -EXE  => Name of executable for compression utility to use.
          :            Will supercede those in @COMPRESSION_UTILS defined by 
          :            this module. If the absolute path to the executable is not provided,
          :            it will be searched in the PATH env variable.
Throws    : Exception if file cannot be compressed.
          : If user is not owner of the file, generates a warning and compresses to
          : a tmp file. To avoid this warning, use the -o file test operator 
          : and call this function with -TMP=>1.
Comments  : Attempts to compress using utilities defined in the @COMPRESSION_UTILS 
          : defined by this module, in the order defined. The first utility that is 
          : found to be executable will be used. Any utility defined in optional -EXE param
          : will be tested for executability first. 
          : To minimize security risks, the -EXE parameter value is untained using
          : the untaint() method of this module (in 'relaxed' mode to permit path separators).

uncompress

Title     : uncompress
Usage     : $Util->uncompress(full-path-filename);
          : $Util->uncompress(<named parameters>);
Purpose   : Uncompress a file.
Example   : $Util->uncompress("/usr/people/me/data.txt");
          : $Util->uncompress(-file=>"/usr/people/me/data.txt.gz",
          :                   -tmp=>1,
          :                   -outfile=>"/usr/people/share/data.txt",
          :                   -exe=>"/usr/local/bin/fancyzip");
Returns   : String containing full, absolute path to uncompressed file
Argument  : Named parameters (case-insensitive):
          :   -FILE => String (name of file to be uncompressed, full path).
          :            If the supplied filename ends with '.gz' or '.Z',
          :            that extension will be removed before attempting to uncompress.
          : Optional:
          :   -TMP  => boolean. If true, (or if user is not the owner of the file)
          :            the file is uncompressed to a temp file. If false, file may be
          :            clobbered with the uncompressed version (if using a utility like
          :            gzip, which is the default)
          :   -OUTFILE => String (name of the output uncompressed file, full path).
          :   -EXE  => Name of executable for uncompression utility to use.
          :            Will supercede those in @UNCOMPRESSION_UTILS defined by 
          :            this module. If the absolute path to the executable is not provided,
          :            it will be searched in the PATH env variable.
Throws    : Exception if file cannot be uncompressed.
          : If user is not owner of the file, generates a warning and uncompresses to
          : a tmp file. To avoid this warning, use the -o file test operator 
          : and call this function with -TMP=>1.
Comments  : Attempts to uncompress using utilities defined in the @UNCOMPRESSION_UTILS 
          : defined by this module, in the order defined. The first utility that is 
          : found to be executable will be used. Any utility defined in optional -EXE param
          : will be tested for executability first. 
          : To minimize security risks, the -EXE parameter value is untained using
          : the untaint() method of this module (in 'relaxed' mode to permit path separators).

file_date

Title    : file_date
Usage    : $Util->file_date( filename [,date_format])
Purpose  : Obtains the date of a given file.
         : Provides flexible formatting via date_format().
Returns  : String = date of the file as: yyyy-mm-dd (e.g., 1997-10-15)
Argument : filename = string, full path name for file
         : date_format = string, desired format for date (see date_format()).
         :               Default = yyyy-mm-dd
Thows    : Exception if no file is provided or does not exist.
Comments : Uses the mtime field as obtained by stat().

untaint

Title   : untaint
Purpose : To remove nasty shell characters from untrusted data
        : and allow a script to run with the -T switch.
        : Potentially dangerous shell meta characters:  &;`'\"|*?!~<>^()[]{}$\n\r
        : Accept only the first block of contiguous characters:
        :  Default allowed chars = "-\w.', ()"
        :  If $relax is true  = "-\w.', ()\/=%:^<>*"
Usage   : $Util->untaint($value, $relax)
Returns : String containing the untained data.
Argument: $value = string
        : $relax = boolean
Comments:
    This general untaint() function may not be appropriate for every situation.
    To allow only a more restricted subset of special characters
    (for example, untainting a regular expression), then using a custom
    untainting mechanism would permit more control.

    Note that special trusted vars (like $0) require untainting.

mean_stdev

Title    : mean_stdev
Usage    : ($mean, $stdev) = $Util->mean_stdev( @data )
Purpose  : Calculates the mean and standard deviation given a list of numbers.
Returns  : 2-element list (mean, stdev)
Argument : list of numbers (ints or floats)
Thows    : n/a

count_files

Title    : count_files
Purpose  : Counts the number of files/directories within a given directory.
         : Also reports the number of text and binary files in the dir
         : as well as names of these files and directories.
Usage    : count_files(\%data)
         :   $data{-DIR} is the directory to be analyzed. Default is ./
         :   $data{-PRINT} = 0|1; if 1, prints results to STDOUT, (default=0).
Argument : Hash reference (empty)
Returns  : n/a;
         : Modifies the hash ref passed in as the sole argument.
         :  $$href{-TOTAL}            scalar
         :  $$href{-NUM_TEXT_FILES}   scalar
         :  $$href{-NUM_BINARY_FILES} scalar
         :  $$href{-NUM_DIRS}         scalar
         :  $$href{-T_FILE_NAMES}     array ref
         :  $$href{-B_FILE_NAMES}     array ref
         :  $$href{-DIRNAMES}         array ref

create_filehandle

Usage     : $object->create_filehandle(<named parameters>);
Purpose   : Create a FileHandle object from a file or STDIN.
          : Mainly used as a helper method by read() and get_newline().
Example   : $data = $object->create_filehandle(-FILE =>'usr/people/me/data.txt')
Argument  : Named parameters (case-insensitive):
          :  (all optional)
          :    -CLIENT  => object reference for the object submitting
          :                the request. Default = $Util.
          :    -FILE    => string (full path to file) or a reference
          :                to a FileHandle object or typeglob. This is an
          :                optional parameter (if not defined, STDIN is used).
Returns   : Reference to a FileHandle object.
Throws    : Exception if cannot open a supplied file or if supplied with a
          : reference that is not a FileHandle ref.
Comments  : If given a FileHandle reference, this method simply returns it.
          : This method assumes the user wants to read ascii data. So, if
          : the file is binary, it will be treated as a compressed (gzipped)
          : file and access it using gzip -ce. The problem here is that not
          : all binary files are necessarily compressed. Therefore,
          : this method should probably have a -mode parameter to
          : specify ascii or binary.

get_newline

Usage     : $object->get_newline(<named parameters>);
Purpose   : Determine the character(s) used for newlines in a given file or
          : input stream. Delegates to Bio::Root::Utilities::get_newline()
Example   : $data = $object->get_newline(-CLIENT => $anObj,
          :                                   -FILE =>'usr/people/me/data.txt')
Argument  : Same arguemnts as for create_filehandle().
Returns   : Reference to a FileHandle object.
Throws    : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline().

taste_file

Usage     : $object->taste_file( <FileHandle> );
          : Mainly a utility method for get_newline().
Purpose   : Sample a filehandle to determine the character(s) used for a newline.
Example   : $char = $Util->taste_file($FH)
Argument  : Reference to a FileHandle object.
Returns   : String containing an octal represenation of the newline character string.
          :   Unix = "\012"  ("\n")
          :   Win32 = "\012\015" ("\r\n")
          :   Mac = "\015"  ("\r")
Throws    : Exception if no input is read within $TIMEOUT_SECS seconds.
          : Exception if argument is not FileHandle object reference.
          : Warning if cannot determine neewline char(s).
Comments  : Based on code submitted by Vicki Brown (vlb@deltagen.com).

file_flavor

Usage     : $object->file_flavor( <filename> );
Purpose   : Returns the 'flavor' of a given file (unix, dos, mac)
Example   : print "$file has flavor: ", $Util->file_flavor($file);
Argument  : filename = string, full path name for file
Returns   : String describing flavor of file and handy info about line endings.
          : One of these is returned:
          :   unix (\n or 012 or ^J)
          :   dos (\r\n or 015,012 or ^M^J)
          :   mac (\r or 015 or ^M)
          :   unknown
Throws    : Exception if argument is not a file
          : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline().

mail_authority

Title    : mail_authority
Usage    : $Util->mail_authority( $message )
Purpose  : Syntactic sugar to send email to $Bio::Root::Global::AUTHORITY

authority

Title    : authority
Usage    : $Util->authority('admin@example.com');
Purpose  : Set/get the email address that should be notified by mail_authority()

send_mail

Title    : send_mail
Usage    : $Util->send_mail( named_parameters )
Purpose  : Provides an interface to mail or sendmail, if available
Returns  : n/a
Argument : Named parameters:  (case-insensitive)
         :  -TO   => e-mail address to send to
         :  -SUBJ => subject for message  (optional)
         :  -MSG  => message to be sent   (optional)
         :  -CC   => cc: e-mail address   (optional)
Thows    : Exception if TO: address appears bad or is missing.
         : Exception if mail cannot be sent.
Comments : Based on  TomC's tip at:
         :   http://www.perl.com/CPAN/doc/FMTEYEWTK/safe_shellings
         :
         : Using default 'From:' information.
         :   sendmail options used:
         :      -t: ignore the address given on the command line and
         :          get To:address from the e-mail header.
         :     -oi: prevents send_mail from ending the message if it
         :          finds a period at the start of a line.

find_exe

Title     : find_exe
Usage     : $Util->find_exe(name);
Purpose   : Locate an executable (for use in a system() call, e.g.))
Example   : $Util->find_exe("gzip");
Returns   : String containing executable that passes the -x test.
            Returns undef if an executable of the supplied name cannot be found.
Argument  : Name of executable to be found.
          : Can be a full path. If supplied name is not executable, an executable
          : of that name will be searched in all directories in the currently
          : defined PATH environment variable.
Throws    : No exceptions, but issues a warning if multiple paths are found
          : for a given name. The first one is used.
Comments  : TODO: Confirm functionality on all bioperl-supported platforms.
            May get tripped up by variation in path separator character used
            for splitting ENV{PATH}.
See Also   :

yes_reply

Title   : yes_reply()
Usage   : $Util->yes_reply( [query_string]);
Purpose : To test an STDIN input value for affirmation.
Example : print +( $Util->yes_reply('Are you ok') ? "great!\n" : "sorry.\n" );
        : $Util->yes_reply('Continue') || die;
Returns : Boolean, true (1) if input string begins with 'y' or 'Y'
Argument: query_string = string to be used to prompt user (optional)
        : If not provided, 'Yes or no' will be used.
        : Question mark is automatically appended.

request_data

Title   : request_data()
Usage   : $Util->request_data( [value_name]);
Purpose : To request data from a user to be entered via keyboard (STDIN).
Example : $name = $Util->request_data('Name');
        : # User will see: % Enter Name:
Returns : String, (data entered from keyboard, sans terminal newline.)
Argument: value_name = string to be used to prompt user.
        : If not provided, 'data' will be used, (not very helpful).
        : Question mark is automatically appended.

verify_version

Purpose : Checks the version of Perl used to invoke the script.
        : Aborts program if version is less than the given argument.
Usage   : verify_version('5.000')

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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