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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::Utils::IO

SYNOPSIS

	use Bio::EnsEMBL::Utils::IO qw/slurp work_with_file slurp_to_array fh_to_array/;
	#or
	# use Bio::EnsEMBL::Utils::IO qw/:slurp/; # brings in any method starting with slurp
	# use Bio::EnsEMBL::Utils::IO qw/:array/; # brings in any method which ends with _array
	# use Bio::EnsEMBL::Utils::IO qw/:gz/;    # brings all methods which start with gz_
	# use Bio::EnsEMBL::Utils::IO qw/:bz/;    # brings all methods which start with bz_
	# use Bio::EnsEMBL::Utils::IO qw/:zip/;   # brings all methods which start with zip_
	# use Bio::EnsEMBL::Utils::IO qw/:all/;   # brings all methods in

  # As a scalar
  my $file_contents = slurp('/my/file/location.txt');
  print length($file_contents);

  # As a ref
  my $file_contents_ref = slurp('/my/file/location.txt', 1);
  print length($$file_contents_ref);

  # Sending it to an array
  my $array = slurp_to_array('/my/location');
  work_with_file('/my/location', 'r', sub {
    $array = process_to_array($_[0], sub {
      #Gives us input line by line
      return "INPUT: $_";
    });
  });

  # Simplified vesion but without the post processing
  $array = fh_to_array($fh);

  # Sending this back out to another file
  work_with_file('/my/file/newlocation.txt', 'w', sub {
    my ($fh) = @_;
    print $fh $$file_contents_ref;
    return;
  });

  # Gzipping the data to another file
  gz_work_with_file('/my/file.gz', 'w', sub {
    my ($fh) = @_;
    print $fh $$file_contents_ref;
    return;
  });

  # Working with a set of lines manually
  work_with_file('/my/file', 'r', sub {
    my ($fh) = @_;
    iterate_lines($fh, sub {
      my ($line) = @_;
      print $line; #Send the line in the file back out
      return;
    });
    return;
  });

  # Doing the same in one go
  iterate_file('/my/file', sub {
    my ($line) = @_;
    print $line; #Send the line in the file back out
    return;
  });

  # Move all data from one file handle to another. Bit like a copy
  move_data($src_fh, $trg_fh);

DESCRIPTION

A collection of subroutines aimed to helping IO based operations

METHODS

See subroutines.

MAINTAINER

$Author$

VERSION

$Revision$

slurp()

Arg [1]     : string $file
Arg [2]     : boolean; $want_ref
Arg [3]     : boolean; $binary
              Indicates if we want to return a scalar reference
Description : Forces the contents of a file into a scalar. This is the
              fastest way to get a file into memory in Perl. You can also
              get a scalar reference back to avoid copying the file contents
              in Scalar references. If the input file is binary then specify
              with the binary flag
Returntype  : Scalar or reference of the file contents depending on arg 2
Example     : my $contents = slurp('/tmp/file.txt');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

spurt()

Arg [1]     : string $file
Arg [2]     : string $contents
Arg [3]     : boolean; $append
Arg [4]     : boolean; $binary
Description : Convenient method to safely open a file and dump some content into it.
              $append can be set to append to the file instead of resetting it first.
              $binary can be set if the content you are printing is not plain-text.
Returntype  : None
Example     : spurt('/tmp/file.txt', $contents);
Exceptions  : If the file could not be created or was not writable
Status      : Stable

gz_slurp

Arg [1]     : string $file
Arg [2]     : boolean; $want_ref Indicates if we want to return a scalar reference
Arg [3]     : boolean; $binary
Arg [4]     : HashRef arguments to pass into IO compression layers
Description : Forces the contents of a file into a scalar. This is the
              fastest way to get a file into memory in Perl. You can also
              get a scalar reference back to avoid copying the file contents
              in Scalar references. If the input file is binary then specify
              with the binary flag
Returntype  : Scalar or reference of the file contents depending on arg 2
Example     : my $contents = slurp('/tmp/file.txt.gz');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

bz_slurp

Arg [1]     : string $file
Arg [2]     : boolean; $want_ref Indicates if we want to return a scalar reference
Arg [3]     : boolean; $binary
Arg [4]     : HashRef arguments to pass into IO compression layers
Description : Forces the contents of a file into a scalar. This is the
              fastest way to get a file into memory in Perl. You can also
              get a scalar reference back to avoid copying the file contents
              in Scalar references. If the input file is binary then specify
              with the binary flag
Returntype  : Scalar or reference of the file contents depending on arg 2
Example     : my $contents = slurp('/tmp/file.txt.bz2');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

zip_slurp

Arg [1]     : string $file
Arg [2]     : boolean; $want_ref Indicates if we want to return a scalar reference
Arg [3]     : boolean; $binary
Arg [4]     : HashRef arguments to pass into IO compression layers
Description : Forces the contents of a file into a scalar. This is the
              fastest way to get a file into memory in Perl. You can also
              get a scalar reference back to avoid copying the file contents
              in Scalar references. If the input file is binary then specify
              with the binary flag
Returntype  : Scalar or reference of the file contents depending on arg 2
Example     : my $contents = slurp('/tmp/file.txt.zip');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

slurp_to_array

Arg [1]     : string $file
Arg [2]     : boolean $chomp
Description : Sends the contents of the given file into an ArrayRef
Returntype  : ArrayRef
Example     : my $contents_array = slurp_to_array('/tmp/file.txt');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

gz_slurp_to_array

Arg [1]     : string $file
Arg [2]     : boolean $chomp
Arg [3]     : HashRef arguments to pass into IO compression layers
Description : Sends the contents of the given gzipped file into an ArrayRef
Returntype  : ArrayRef
Example     : my $contents_array = gz_slurp_to_array('/tmp/file.txt.gz');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

bz_slurp_to_array

Arg [1]     : string $file
Arg [2]     : boolean $chomp
Arg [3]     : HashRef arguments to pass into IO compression layers
Description : Sends the contents of the given bzipped file into an ArrayRef
Returntype  : ArrayRef
Example     : my $contents_array = bz_slurp_to_array('/tmp/file.txt.bz2');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

zip_slurp_to_array

Arg [1]     : string $file
Arg [2]     : boolean $chomp
Arg [3]     : HashRef arguments to pass into IO compression layers
Description : Sends the contents of the given zipped file into an ArrayRef
Returntype  : ArrayRef
Example     : my $contents_array = zip_slurp_to_array('/tmp/file.txt.zip');
Exceptions  : If the file did not exist or was not readable
Status      : Stable

fh_to_array

Arg [1]     : Glob/IO::Handle $fh
Arg [2]     : boolean $chomp
Description : Sends the contents of the given filehandle into an ArrayRef.
              Will perform chomp on each line if specified. If you require
              any more advanced line based processing then see
              L<process_to_array>.
Returntype  : ArrayRef
Example     : my $contents_array = fh_to_array($fh);
Exceptions  : None
Status      : Stable

process_to_array

Arg [1]     : Glob/IO::Handle $fh
Arg [2]     : CodeRef $callback
Description : Sends the contents of the given file handle into an ArrayRef
              via the processing callback. Assumes line based input.
Returntype  : ArrayRef
Example     : my $array = process_to_array($fh, sub { return "INPUT: $_"; });
Exceptions  : If the fh did not exist or if a callback was not given.
Status      : Stable

iterate_lines

Arg [1]     : Glob/IO::Handle $fh
Arg [2]     : CodeRef $callback
Description : Iterates through each line from the given file handle and
              hands them to the callback one by one
Returntype  : None
Example     : iterate_lines($fh, sub { print "INPUT: $_"; });
Exceptions  : If the fh did not exist or if a callback was not given.
Status      : Stable

iterate_file

Arg [1]     : string $file
Arg [3]     : CodeRef the callback which is used to iterate the lines in
              the file
Description : Iterates through each line from the given file and
              hands them to the callback one by one
Returntype  : None
Example     : iterate_file('/my/file', sub { print "INPUT: $_"; });
Exceptions  : If the file did not exist or if a callback was not given.
Status      : Stable

work_with_file

Arg [1]     : string $file
Arg [2]     : string; $mode
              Supports all modes specified by the C<open()> function as well as those
              supported by IO::File
Arg [3]     : CodeRef the callback which is given the open file handle as
              its only argument
Description : Performs the nitty gritty of checking if a file handle is open
              and closing the resulting filehandle down.
Returntype  : None
Example     : work_with_file('/tmp/out.txt', 'w', sub {
                my ($fh) = @_;
                print $fh 'hello';
                return;
              });
Exceptions  : If we could not work with the file due to permissions
Status      : Stable

gz_work_with_file

Arg [1]     : string $file
Arg [2]     : string; $mode
              Supports modes like C<r>, C<w>, C<\>> and C<\<>
Arg [3]     : CodeRef the callback which is given the open file handle as
              its only argument
Arg [4]     : HashRef used to pass options into the IO
              compression/uncompression modules
Description : Performs the nitty gritty of checking if a file handle is open
              and closing the resulting filehandle down.
Returntype  : None
Example     : gz_work_with_file('/tmp/out.txt.gz', 'w', sub {
                my ($fh) = @_;
                print $fh 'hello';
                return;
              });
Exceptions  : If we could not work with the file due to permissions
Status      : Stable

bz_work_with_file

Arg [1]     : string $file
Arg [2]     : string; $mode
              Supports modes like C<r>, C<w>, C<\>> and C<\<>
Arg [3]     : CodeRef the callback which is given the open file handle as
              its only argument
Arg [4]     : HashRef used to pass options into the IO
              compression/uncompression modules
Description : Performs the nitty gritty of checking if a file handle is open
              and closing the resulting filehandle down.
Returntype  : None
Example     : bz_work_with_file('/tmp/out.txt.bz2', 'w', sub {
                my ($fh) = @_;
                print $fh 'hello';
                return;
              });
Exceptions  : If we could not work with the file due to permissions
Status      : Stable

zip_work_with_file

Arg [1]     : string $file
Arg [2]     : string; $mode
              Supports modes like C<r>, C<w>, C<\>> and C<\<>
Arg [3]     : CodeRef the callback which is given the open file handle as
              its only argument
Arg [4]     : HashRef used to pass options into the IO
              compression/uncompression modules
Description : Performs the nitty gritty of checking if a file handle is open
              and closing the resulting filehandle down.
Returntype  : None
Example     : zip_work_with_file('/tmp/out.txt.zip', 'w', sub {
                my ($fh) = @_;
                print $fh 'hello';
                return;
              });
Exceptions  : If we could not work with the file due to permissions
Status      : Stable

filter_dir

Arg [1]     : String; directory
Arg [2]     : CodeRef; the callback which is given a file in the
              directory as its only argument
Description : Return the lexicographically sorted content of a directory.
              The callback allows to specify the criteria an entry in
              the directory must satisfy in order to appear in the content.
Returntype  : Arrayref; list with the filtered files/directory
Example     : filter_dir('/tmp', sub {
                my $file = shift;

                # select perl scripts in the directory
                return $file if $file =~ /\.pl$/;
              });
Exceptions  : If the directory cannot be opened or its handle
              cannot be closed
Status      : Stable

move_data

Arg [1]     : FileHandle $src_fh
Arg [2]     : FileHandle $trg_fh
Arg [3]     : int $buffer. Defaults to 8KB
Description : Moves data from the given source filehandle to the target one
              using a 8KB buffer or user specified buffer
Returntype  : None
Example     : move_data($src_fh, $trg_fh, 16*1024); # copy in 16KB chunks
Exceptions  : If inputs were not as expected

cpanm Bio::EnsEMBL::CDS

perl -MCPAN -e shell
install Bio::EnsEMBL::CDS