Bio PullParserI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::PullParserI - A base module for fast 'pull' parsing
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Inherit
Bio::Root::RootI
Synopsis
    # do not use this class, it is intended for parser module
# writers only
Description
If you are writing a module to parse some new format, you may wish to use
a 'pull' approach whereby you only do work (reading file data, parsing it,
turning the parsed data in an object) when absolutely necessary.
PullParserI provides a system for doing exactly that. As a PullParser you
need a chunk. A chunk is just a Bio::Root::IO that contains all the raw data
you would want to parse. You can use the chunk() method to create a chunk from
a filename, existing filehandle or even a string. If you make a chunk from a
large file, but actually only want your chunk to be some portion of the whole
file, supply start and end amounts in bytes to chunk() at the same time.
The methods _chunk_seek() and _chunk_tell() provide seeks and tells that are
relative to the start and end of your chunk, not the whole file.
The other thing you will need to decide when making a chunk is how to handle
piped input. A PullParser typically needs seekable data to parse, so if your
data is piped in and unseekable, you must decide between creating a temp file
or reading the input into memory, which will be done before the chunk becomes
usable and you can begin any parsing. Alternatively you can choose to force
a sequential read, in which case you can make use of _dependencies() to define
the linear order of methods that would result in the file being read
sequentially. The return value of _sequential() is also useful here, if you
would need to cache some data or otherwise behave differently during a
sequential read.
The main method in the system is get_field(). This method relies on the
existance of a private hash reference accessible to it with the method
_fields(). That hash ref should have as keys all the sorts of data you will want
to parse (eg. 'score'), and prior to parsing the values would be undefined. A
user of your module can then call either $module->get_field('score') or
$module->score and get_field will either return the answer from
$self->_fields->{score} if it is defined, or call a method _discover_score()
first if not. So for the system to work you need to define a _discover_*()
method for every field in the fields hash, and ensure that the method stores an
answer in the fields hash.
How you implement your _discover_* methods is up to you, though you should never
call a _discover_* method directly yourself; always use get_field(), since
get_field() will deal with calling dependent methods for you if a forced
sequenctial read is in progress due to piped input. You will almost certainly
want to make use of the various chunk-related methods of this class (that are
denoted private by the leading '_'; this means you can use them as the author of
a parser class, but users of your parser should not).
Primary amongst them is _*_chunk_by_end() to which you provide text that
represents the end of your desired chunk and it does a readline with your
argument as $/. The chunk knows about its line-endings, so if you want your
end definition to include a new line, just always use "\n" and PullParserI will
do any necessary conversion for you.
If your input data is hierarchical (eg. report->many results->many hits->many
hsps), and you want an object at the leaf of the hierarchy to have access to
information that is shared amongst all of them (is parsed in the root), you
don't have to copy the data to each leaf object; simply by defining parent(),
when you call get_field() and the requested field isn't in your leaf's fields
hash, the leaf's parent will be asked for the field instead, and so on till
root.
See Bio::SearchIO::hmmer_pull for an example of implementing a parser using
PullParserI.
Methods
BEGIN Code
_fieldsDescriptionCode
has_fieldDescriptionCode
get_fieldDescriptionCode
parentDescriptionCode
chunkDescriptionCode
_sequentialDescriptionCode
_dependenciesDescriptionCode
_chunk_true_startDescriptionCode
_chunk_true_endDescriptionCode
_line_endingDescriptionCode
_chunk_seekDescriptionCode
_chunk_tellDescriptionCode
_get_chunk_by_nolDescriptionCode
_get_chunk_by_endDescriptionCode
_find_chunk_by_endDescriptionCode
AUTOLOADDescriptionCode
Methods description
_fieldscode    nextTop
 Title   : _fields
Usage : $obj->_fields( { field1 => undef } );
my $fields_ref = $obj->_fields;
Function: Get/set the hash reference containing all the fields for this parser
Returns : hash ref
Args : none to get, OR hash ref to set
has_fieldcodeprevnextTop
 Title   : has_field
Usage : if ($obj->has_field('field_name') {...}
Function: Ask if a particular object has a given field (doesn't ask ancestors)
Returns : boolean
Args : string (the field name to test)
get_fieldcodeprevnextTop
 Title   : get_field
Usage : my $field_value = $obj->get_field('field_name');
Function: Get the value of a given field. If this $obj doesn't have the field,
it's parent() will be asked, and so on until there are no more
parents.
Returns : scalar, warns if a value for the field couldn't be found and returns
undef.
Args : string (the field to get)
parentcodeprevnextTop
 Title   : parent
Usage : $obj->parent($parent_obj);
my $parent_obj = $obj->parent;
Function: Get/set the parent object of this one.
Returns : Bio::PullParserI
Args : none to get, OR Bio::PullParserI to set
chunkcodeprevnextTop
 Title   : chunk
Usage : $obj->chunk($filename);
my $chunk = $obj->chunk;
Function: Get/set the chunk of this parser.
Returns : Bio:Root::IO
Args : none to get, OR
First argument of a GLOB reference, filename string, string data to
treat as the chunk, or Bio::Root::IO.
Optionally, also provide:
-start => int : the byte position within the thing described by the
first argument to consider as the start of this
chunk (default 0)
-end => int : the byte position to consider as the end (default
true end)
-piped_behaviour => 'memory'|'temp_file'|'sequential_read'
The last option comes into effect when the first argument is something that cannot be seeked (eg. piped input filehandle). 'memory' means read all the piped input into a string first, then set the chunk to that string. 'temp_file' means read all the piped input and output it to a temp file, then set the chunk to that temp file. 'sequential_read' means that the piped input should be read sequentially and your parsing code must cope with not being able to seek. 'memory' is the fastest but uses the most memory. 'temp_file' and 'sequential_read' can be slow, with 'temp_file' being the most memory efficient but requiring disc space. The default is 'sequential_read'. Note that in versions of perl earlier than 5.8 only temp_file works and will be used regardless of what value is supplied here.
_sequentialcodeprevnextTop
 Title   : _sequential
Usage : if ($obj->_sequential) {...}
Function: Ask if we have to do operations such that the input is read
sequentially.
Returns : boolean
Args : none to get, OR boolean to set (typically, you should never set this
yourself)
_dependenciescodeprevnextTop
 Title   : _dependencies
Usage : $obj->_dependencies( { field1 => field2 } );
my $dependancy = $obj->_dependencies('field_name');
Function: Set the fields that are dependent on each other, or get the field
than another is dependent upon.
Returns : string (a field name)
Args : string (a field name) to get, OR hash ref to initially set, with
field names as keys and values, key field being dependent upon value
field.
_chunk_true_startcodeprevnextTop
 Title   : _chunk_true_start
Usage : my $true_start = $obj->_chunk_true_start;
Function: Get/set the true start position of the chunk within the filehandle
it is part of.
Returns : int
Args : none to get, OR int to set (typically, you won't set this yourself)
_chunk_true_endcodeprevnextTop
 Title   : _chunk_true_end
Usage : my $true_end = $obj->_chunk_true_end;
Function: Get/set for the true end position of the chunk within the filehandle
it is part of.
Returns : int
Args : none to get, OR int to set (typically, you won't set this yourself)
_line_endingcodeprevnextTop
 Title   : _line_ending
Usage : my $line_ending = $obj->_line_ending;
Function: Get/set for the line ending for the chunk.
Returns : string
Args : none to get, OR string to set (typically, you won't set this
yourself)
_chunk_seekcodeprevnextTop
 Title   : _chunk_seek
Usage : $obj->_chunk_seek($pos);
Function: seek() the chunk to the provided position in bytes, relative to the
defined start of the chunk within its filehandle.
In _sequential() mode, this function does nothing. Returns : n/a Args : int
_chunk_tellcodeprevnextTop
 Title   : _chunk_seek
Usage : my $pos = $obj->_chunk_tell;
Function: Get the current tell() position within the chunk, relative to the
defined start of the chunk within its filehandle.
In _sequential() mode, this function does nothing. Returns : int Args : none
_get_chunk_by_nolcodeprevnextTop
 Title   : _chunk_seek
Usage : my $string = $obj->_get_chunk_by_nol;
Function: Get a chunk of chunk() from the current position onward for the given
number of lines.
Returns : string
Args : int (number of lines you want)
_get_chunk_by_endcodeprevnextTop
 Title   : _get_chunk_by_end
Usage : my $string = $obj->_get_chunk_by_end;
Function: Get a chunk of chunk() from the current position onward till the end
of the line, as defined by the supplied argument.
Returns : string
Args : string (line ending - if you want the line ending to include a new
line, always use \n)
_find_chunk_by_endcodeprevnextTop
 Title   : _find_chunk_by_end
Usage : my $string = $obj->_find_chunk_by_end;
Function: Get the start and end of what would be a chunk of chunk() from the
current position onward till the end of the line, as defined by the
supplied argument.
In _sequential() mode, this function does nothing. Returns : _chunk_tell values for start and end in 2 element list Args : string (line ending - if you want the line ending to include a new line, always use \n)
AUTOLOADcodeprevnextTop
 Title   : AUTOLOAD
Usage : n/a
Function: Assumes that any unknown method called should be treated as
get_field($method_name).
Returns : n/a
Args : n/a
Methods code
BEGINTop
BEGIN {
    # chunk() needs perl 5.8 feature for modes other than temp_file, so will
# workaround by forcing temp_file mode in <5.8. Could also rewrite using
# IO::String, but don't want to.
if ($] < 5.008) { $FORCE_TEMP_FILE = 1;
}
_fieldsdescriptionprevnextTop
sub _fields {
    my $self = shift;
    if (@_) {
        $self->{_fields} = shift;
    }
    unless (defined $self->{_fields}) {
        $self->{_fields} = { };
    }
    return $self->{_fields};
}
has_fielddescriptionprevnextTop
sub has_field {
    my ($self, $desired) = @_;
    $desired || return;
    return exists $self->_fields->{$desired};
}
get_fielddescriptionprevnextTop
sub get_field {
    my $self = shift;
    my $desired = shift || return keys %{$self->_fields};
    if (exists $self->_fields->{$desired}) {
        unless (defined $self->_fields->{$desired}) {
            my $method = '_discover_'.$desired;
            
            my $dependency = $self->_dependencies($desired);
            if ($dependency && ! defined $self->_fields->{$dependency}) {
                $self->get_field($dependency);
            }
            
            # it might exist now
$self->$method unless defined $self->_fields->{$desired}; } return $self->_fields->{$desired}; } # is it a field of our parent? (checks all ancestors)
if (my $parent = $self->parent) { return $parent->get_field($desired); } $desired =~ s/_discover_//; $self->warn("This report does not hold information about '$desired'"); return;
}
parentdescriptionprevnextTop
sub parent {
    my $self = shift;
    if (@_) { $self->{parent} = shift }
    return $self->{parent} || return;
}
chunkdescriptionprevnextTop
sub chunk {
    my $self = shift;
    
    if (@_) {
        my $thing = shift || $self->throw("Trying to set chunk() to an undefined value");
        if (ref($thing) eq 'GLOB') {
            $self->{_chunk} = Bio::Root::IO->new(-fh => $thing);
        }
        elsif (ref(\$thing) eq 'SCALAR') {
            if ($thing !~ /\n/ && -e $thing) {
                $self->{_chunk} = Bio::Root::IO->new(-file => $thing);
            }
            else {
                unless ($FORCE_TEMP_FILE) {
                    # treat a string as a filehandle
open(my $fake_fh, "+<",\$ thing); # requires perl 5.8
$self->{_chunk} = Bio::Root::IO->new(-fh => $fake_fh); } else { my ($handle) = $self->{_chunk}->tempfile(); print $handle $thing; $self->{_chunk} = Bio::Root::IO->new(-fh => $handle); } } } elsif ($thing->isa('Bio::Root::IO')) { $self->{_chunk} = $thing; } else { $self->throw("Unknown input into chunk()"); } my ($piped_behaviour, $start, $end); if (@_) { ($piped_behaviour, $start, $end) = $self->_rearrange([qw(PIPED_BEHAVIOUR START END)], @_); } $piped_behaviour ||= 'sequential_read'; $FORCE_TEMP_FILE && ($piped_behaviour = 'temp_file'); $start ||= 0; $self->_chunk_true_start($start); $self->_chunk_true_end($end); # determine if the chunk is seekable
my $fh = $self->{_chunk}->_fh; seek($fh, 0, 0); my $first_line = <$fh>; seek($fh, 0, 0); my $seekable = tell($fh) == 0; unless ($seekable) { if ($piped_behaviour eq 'memory') { my $string = $first_line; while (<$fh>) { $string .= $_; } $self->chunk($string); } elsif ($piped_behaviour eq 'temp_file') { my ($handle) = $self->{_chunk}->tempfile(); print $handle $first_line; while (<$fh>) { print $handle $_; } seek($handle, 0, 0); $self->chunk($handle); } elsif ($piped_behaviour eq 'sequential_read') { $self->{_chunk}->_pushback($first_line); $self->_sequential(1); } else { $self->throw("Unknown piped behaviour type '$piped_behaviour'"); } } # determine our line ending
if ($first_line =~ /\r\n/) { $self->_line_ending("\r\n"); } elsif ($first_line =~ /\r/) { $self->_line_ending("\r"); } else { $self->_line_ending("\n"); } } return $self->{_chunk} || return;
}
_sequentialdescriptionprevnextTop
sub _sequential {
    my $self = shift;
    if (@_) {
        $self->{_sequential} = shift;
    }
    return $self->{_sequential} || 0;
}
_dependenciesdescriptionprevnextTop
sub _dependencies {
    my ($self, $thing) = @_;
    $thing || return;
    if (ref($thing) eq 'HASH') {
        $self->{_dependencies} = $thing;
    }
    else {
        return $self->{_dependencies}->{$thing};
    }
}
_chunk_true_startdescriptionprevnextTop
sub _chunk_true_start {
    my $self = shift;
    if (@_) {
        $self->{_chunk_start} = shift;
    }
    return $self->{_chunk_start} || 0;
}
_chunk_true_enddescriptionprevnextTop
sub _chunk_true_end {
    my $self = shift;
    if (@_) {
        $self->{_chunk_end} = shift;
    }
    return $self->{_chunk_end};
}
_line_endingdescriptionprevnextTop
sub _line_ending {
    my $self = shift;
    if (@_) {
        $self->{_chunk_line_ending} = shift;
    }
    return $self->{_chunk_line_ending};
}
_chunk_seekdescriptionprevnextTop
sub _chunk_seek {
    my ($self, $pos) = @_;
    $self->throw("Undefined position passed") unless defined $pos;
    return if $self->_sequential;
    
    my $fh = $self->chunk->_fh;
    
    # seek to the defined start
seek($fh, $self->_chunk_true_start, 0); # now seek to desired position relative to defined start
seek($fh, $pos, 1);
}
_chunk_telldescriptionprevnextTop
sub _chunk_tell {
    my $self = shift;
    return if $self->_sequential;
    
    my $fh = $self->chunk->_fh;
    return tell($fh) - $self->_chunk_true_start;
}
_get_chunk_by_noldescriptionprevnextTop
sub _get_chunk_by_nol {
    my ($self, $nol) = @_;
    $nol > 0 || $self->throw("Can't request a chunk of fewer than 1 lines");
    
    # hope that $/ is \n
my ($line, $count); while (defined($_ = $self->chunk->_readline)) { $line .= $_; $count++; last if $count == $nol; } my $current = $self->_chunk_tell; my $end = ($current || 0) + $self->_chunk_true_start; if (! $current || ($self->_chunk_true_end ? $end <= $self->_chunk_true_end : 1)) { return $line; } return;
}
_get_chunk_by_enddescriptionprevnextTop
sub _get_chunk_by_end {
    my ($self, $chunk_ending) = @_;
    
    my $start = $self->_chunk_tell;
    
    my $line_ending = $self->_line_ending;
    $chunk_ending =~ s/\n/$line_ending/g;
    local $/ = $chunk_ending || '';
    my $line = $self->chunk->_readline;
    
    my $current = $self->_chunk_tell;
    my $end = ($current || 0) + $self->_chunk_true_start;
    if (! $current || ($self->_chunk_true_end ? $end <= $self->_chunk_true_end : 1)) {
        return $line;
    }
    
    $self->_chunk_seek($start);
    return;
}
_find_chunk_by_enddescriptionprevnextTop
sub _find_chunk_by_end {
    my ($self, $chunk_ending) = @_;
    return if $self->_sequential;
    
    my $line_ending = $self->_line_ending;
    $chunk_ending =~ s/\n/$line_ending/g;
    local $/ = $chunk_ending || '';
    
    my $start = $self->_chunk_tell;
    $self->chunk->_readline;
    my $end = $self->_chunk_tell;
    
    my $comp_end = $end + $self->_chunk_true_start;
    if ($self->_chunk_true_end ? $comp_end <= $self->_chunk_true_end : 1) {
        return ($start, $end);
    }
    
    $self->_chunk_seek($start);
    return;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my $self = shift;
    ref($self) || return;
    
	my $name = $AUTOLOAD;
	$name =~ s/.*://; # strip fully-qualified portion
# is it one of our fields?
return $self->get_field($name); } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
CONTRIBUTORSTop
Inspired by a posting by Aaron J. Mackey
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _