Bio::DB::Flat OBDAIndex
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Summary
Bio::DB::Flat::OBDAIndex - Binary search indexing system for sequence files
Package variables
Privates (from "my" definitions)
@formats = ['FASTA','SWISSPROT','EMBL']
Included modules
Bio::DB::RandomAccessI
Bio::Root::RootI
Bio::Seq
Bio::SeqIO
Fcntl qw ( SEEK_END SEEK_CUR )
Inherit
Bio::DB::RandomAccessI
Synopsis
This module can be used both to index sequence files and also to retrieve
sequences from existing sequence files.
    my $sequencefile;  # Some fasta sequence file
Patterns have to be entered to define where the keys are to be
indexed and also where the start of each record. E.g. for fasta
    my $start_pattern   = "^>";
my $primary_pattern = "^>(\\S+)";
So the start of a record is a line starting with a > and the primary
key is all characters up to the first space afterf the >
A string also has to be entered to defined what the primary key
(primary_namespace) is called.
The index can now be created using
    my $index = new Bio::DB::Flat::OBDAIndex(
-start_pattern => $start_pattern,
-primary_pattern => $primary_pattern,
-primary_namespace => "ACC",
);
To actually write it out to disk we need to enter a directory where the
indices will live, a database name and an array of sequence files to index.
    my @files = ("file1","file2","file3");
$index->make_index("/Users/michele/indices","mydatabase",@files);
The index is now ready to use. For large sequence files the perl
way of indexing takes a *long* time and a *huge* amount of memory.
For indexing things like dbEST I recommend using the C indexer. Sometimes just indexing files with one id per entry is not enough. For
instance you may want to retrieve sequences from swissprot using
their accessions as well as their ids.
To be able to do this when creating your index you need to pass in
a hash of secondary_patterns which have their namespaces as the keys
to the hash.
e.g. For Indexing something like
ID 1433_CAEEL STANDARD; PRT; 248 AA.
AC P41932;
DT 01-NOV-1995 (Rel. 32, Created)
DT 01-NOV-1995 (Rel. 32, Last sequence update)
DT 15-DEC-1998 (Rel. 37, Last annotation update)
DE 14-3-3-LIKE PROTEIN 1.
GN FTT-1 OR M117.2.
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC Rhabditidae; Peloderinae; Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
where we want to index the accession (P41932) as the primary key and the
id (1433_CAEEL) as the secondary id. The index is created as follows
    my %secondary_patterns;
my $start_pattern = "^ID (\\S+)"; my $primary_pattern = "^AC (\\S+)\;"; $secondary_patterns{"ID"} = "^ID (\\S+)"; my $index = new Bio::DB::Flat::OBDAIndex( -start_pattern => $start_pattern, -primary_pattern => $primary_pattern, -primary_namespace => 'ACC', -secondary_patterns => \%secondary_patterns); $index->make_index("/Users/michele/indices","mydb",($seqfile));
Of course having secondary indices makes indexing slower and more
of a memory hog. To fetch sequences using an existing index first of all create your sequence
object
    my $index = new Bio::DB::Flat::OBDAIndex(-index_dir => $index_directory,
-dbname => 'swissprot');
Now you can happily fetch sequences either by the primary key or
by the secondary keys.
    my $entry = $index->get_entry_by_id('HBA_HUMAN');
This returns just a string containing the whole entry. This is
useful is you just want to print the sequence to screen or write it to a file.
Other ways of getting sequences are
    my $fh = $index->get_stream_by_id('HBA_HUMAN');
This can then be passed to a seqio object for output or converting
into objects.
    my $seq = new Bio::SeqIO(-fh     => $fh,
-format => 'fasta');
The last way is to retrieve a sequence directly. This is the
slowest way of extracting as the sequence objects need to be made.
    my $seq = $index->get_Seq_by_id('HBA_HUMAN');
To access the secondary indices the secondary namespace needs to be known
(use $index->secondary_namespaces) and the following call used
    my $seq   = $index->get_Seq_by_secondary('ACC','Q21973');
my $fh = $index->get_stream_by_secondary('ACC','Q21973');
my $entry = $index->get_entry_by_secondary('ACC','Q21973');
Description
This object allows indexing of sequence files both by a primary key
(say accession) and multiple secondary keys (say ids). This is
different from the Bio::Index::Abstract (see Bio::Index::Abstract)
which uses DBM files as storage. This module uses a binary search to
retrieve sequences which is more efficient for large datasets.
Methods
_add_id_positionDescriptionCode
_index_fileDescriptionCode
database_nameDescriptionCode
find_entryDescriptionCode
formatDescriptionCode
get_Seq_by_accDescriptionCode
get_Seq_by_idDescriptionCode
get_Seq_by_secondaryDescriptionCode
get_entry_by_idDescriptionCode
get_filehandle_by_fileidDescriptionCode
get_fileid_by_filenameDescriptionCode
get_stream_by_idDescriptionCode
index_directoryDescriptionCode
index_typeDescriptionCode
index_versionDescriptionCode
make_config_fileDescriptionCode
make_indexDescriptionCode
make_indexdirDescriptionCode
newDescriptionCode
new_EMBL_index
No description
Code
new_FASTA_index
No description
Code
new_SWISSPROT_index
No description
Code
new_from_registry
No description
Code
new_secondary_filehandleDescriptionCode
open_secondary_indexDescriptionCode
primary_index_fileDescriptionCode
primary_index_filehandleDescriptionCode
primary_namespaceDescriptionCode
primary_patternDescriptionCode
read_config_fileDescriptionCode
read_headerDescriptionCode
read_recordDescriptionCode
record_sizeDescriptionCode
secondary_namespacesDescriptionCode
secondary_patternsDescriptionCode
start_patternDescriptionCode
syseof
No description
Code
systell
No description
Code
write_primary_indexDescriptionCode
write_secondary_indicesDescriptionCode
Methods description
_add_id_positioncode    nextTop
 Title   : _add_id_position
Usage : $obj->_add_id_position($newval)
Function:
Example :
Returns : value of _add_id_position
Args : newvalue (optional)
_index_filecodeprevnextTop
 Title   : _index_file
Usage : $obj->_index_file($newval)
Function:
Example :
Returns : value of _index_file
Args : newvalue (optional)
database_namecodeprevnextTop
 Title   : database_name
Usage : $obj->database_name($newval)
Function:
Example :
Returns : value of database_name
Args : newvalue (optional)
find_entrycodeprevnextTop
 Title   : find_entry
Usage : $obj->find_entry($newval)
Function:
Example :
Returns : value of find_entry
Args : newvalue (optional)
formatcodeprevnextTop
 Title   : format
Usage : $obj->format($newval)
Function:
Example :
Returns : value of format
Args : newvalue (optional)
get_Seq_by_acccodeprevnextTop
 Title   : get_Seq_by_acc
Usage : $obj->get_Seq_by_acc($newval)
Function:
Example :
Returns : value of get_Seq_by_acc
Args : newvalue (optional)
get_Seq_by_idcodeprevnextTop
 Title   : get_Seq_by_id
Usage : $obj->get_Seq_by_id($newval)
Function:
Example :
Returns : value of get_Seq_by_id
Args : newvalue (optional)
get_Seq_by_secondarycodeprevnextTop
 Title   : get_Seq_by_secondary
Usage : $obj->get_Seq_by_secondary($newval)
Function:
Example :
Returns : value of get_Seq_by_secondary
Args : newvalue (optional)
get_entry_by_idcodeprevnextTop
 Title   : get_entry_by_id
Usage : $obj->get_entry_by_id($newval)
Function:
Example :
Returns :
Args :
get_filehandle_by_fileidcodeprevnextTop
 Title   : get_filehandle_by_fileid
Usage : $obj->get_filehandle_by_fileid($newval)
Function:
Example :
Returns : value of get_filehandle_by_fileid
Args : newvalue (optional)
get_fileid_by_filenamecodeprevnextTop
 Title   : get_fileid_by_filename
Usage : $obj->get_fileid_by_filename($newval)
Function:
Example :
Returns : value of get_fileid_by_filename
Args : newvalue (optional)
get_stream_by_idcodeprevnextTop
 Title   : get_stream_by_id
Usage : $obj->get_stream_by_id($newval)
Function:
Example :
Returns : value of get_stream_by_id
Args : newvalue (optional)
index_directorycodeprevnextTop
 Title   : index_directory
Usage : $obj->index_directory($newval)
Function:
Example :
Returns : value of index_directory
Args : newvalue (optional)
index_typecodeprevnextTop
 Title   : index_type
Usage : $obj->index_type($newval)
Function:
Example :
Returns : value of index_type
Args : newvalue (optional)
index_versioncodeprevnextTop
 Title   : index_version
Usage : $obj->index_version($newval)
Function:
Example :
Returns : value of index_version
Args : newvalue (optional)
make_config_filecodeprevnextTop
 Title   : make_config_file
Usage : $obj->make_config_file($newval)
Function:
Example :
Returns : value of make_config_file
Args : newvalue (optional)
make_indexcodeprevnextTop
 Title   : make_index
Usage : $obj->make_index($newval)
Function:
Example :
Returns : value of make_index
Args : newvalue (optional)
make_indexdircodeprevnextTop
 Title   : make_indexdir
Usage : $obj->make_indexdir($newval)
Function:
Example :
Returns : value of make_indexdir
Args : newvalue (optional)
newcodeprevnextTop
 Title   : new
Usage : For reading
my $index = new Bio::DB::Flat::OBDAIndex(
-index_dir => '/Users/michele/indices/',
-dbname => 'dbEST',
-format => 'fasta');
For writing my %secondary_patterns = {"ACC" => "^>\\S+ +(\\S+)"} my $index = new Bio::DB::Flat::OBDAIndex( -index_dir => '/Users/michele/indices', -primary_pattern => "^>(\\S+)", -secondary_patterns => \%secondary_patterns, -primary_namespace => "ID"); my @files = ('file1','file2','file3'); $index->make_index('mydbname',@files); Function: create a new Bio::DB::Flat::OBDAIndex object Returns : new Bio::DB::Flat::OBDAIndex Args : -index_dir Directory containing the indices -primary_pattern Regexp defining the primary id -secondary_patterns A hash ref containing the secondary patterns with the namespaces as keys -primary_namespace A string defining what the primary key is Status : Public
new_secondary_filehandlecodeprevnextTop
 Title   : new_secondary_filehandle
Usage : $obj->new_secondary_filehandle($newval)
Function:
Example :
Returns : value of new_secondary_filehandle
Args : newvalue (optional)
open_secondary_indexcodeprevnextTop
 Title   : open_secondary_index
Usage : $obj->open_secondary_index($newval)
Function:
Example :
Returns : value of open_secondary_index
Args : newvalue (optional)
primary_index_filecodeprevnextTop
 Title   : primary_index_file
Usage : $obj->primary_index_file($newval)
Function:
Example :
Returns : value of primary_index_file
Args : newvalue (optional)
primary_index_filehandlecodeprevnextTop
 Title   : primary_index_filehandle
Usage : $obj->primary_index_filehandle($newval)
Function:
Example :
Returns : value of primary_index_filehandle
Args : newvalue (optional)
primary_namespacecodeprevnextTop
 Title   : primary_namespace
Usage : $obj->primary_namespace($newval)
Function:
Example :
Returns : value of primary_namespace
Args : newvalue (optional)
primary_patterncodeprevnextTop
 Title   : primary_pattern
Usage : $obj->primary_pattern($newval)
Function:
Example :
Returns : value of primary_pattern
Args : newvalue (optional)
read_config_filecodeprevnextTop
 Title   : read_config_file
Usage : $obj->read_config_file($newval)
Function:
Example :
Returns : value of read_config_file
Args : newvalue (optional)
read_headercodeprevnextTop
 Title   : read_header
Usage : $obj->read_header($newval)
Function:
Example :
Returns : value of read_header
Args : newvalue (optional)
read_recordcodeprevnextTop
 Title   : read_record
Usage : $obj->read_record($newval)
Function:
Example :
Returns : value of read_record
Args : newvalue (optional)
record_sizecodeprevnextTop
 Title   : record_size
Usage : $obj->record_size($newval)
Function:
Example :
Returns : value of record_size
Args : newvalue (optional)
secondary_namespacescodeprevnextTop
 Title   : secondary_namespaces
Usage : $obj->secondary_namespaces($newval)
Function:
Example :
Returns : value of secondary_namespaces
Args : newvalue (optional)
secondary_patternscodeprevnextTop
 Title   : secondary_patterns
Usage : $obj->secondary_patterns($newval)
Function:
Example :
Returns : value of secondary_patterns
Args : newvalue (optional)
start_patterncodeprevnextTop
 Title   : start_pattern
Usage : $obj->start_pattern($newval)
Function:
Example :
Returns : value of start_pattern
Args : newvalue (optional)
write_primary_indexcodeprevnextTop
 Title   : write_primary_index
Usage : $obj->write_primary_index($newval)
Function:
Example :
Returns : value of write_primary_index
Args : newvalue (optional)
write_secondary_indicescodeprevnextTop
 Title   : write_secondary_indices
Usage : $obj->write_secondary_indices($newval)
Function:
Example :
Returns : value of write_secondary_indices
Args : newvalue (optional)
Methods code
_add_id_positiondescriptionprevnextTop
sub _add_id_position {
    my ($self,$id,$pos,$fileid,$length,$secondary_id) = @_;

    if (!defined($id)) {
	$self->throw("No id defined. Can't add id position");
    }
    if (!defined($pos)) {
v	$self->throw("No position defined. Can't add id position");
    }
    if (!defined($fileid)) {
	$self->throw("No fileid defined. Can't add id position");
    }
    if (!defined($length) || $length <= 0) {
	$self->throw("No length defined or <= 0 [$length]. Can't add id position");
    }

    $self->{_id}{$id}{_pos}    = $pos;
    $self->{_id}{$id}{_length} = $length;
    $self->{_id}{$id}{_fileid} = $fileid;
    
    # Now the secondary ids
foreach my $sec (keys (%$secondary_id)) { my $value = $secondary_id->{$sec}; $self->{_secondary_id}{$sec}{$value}{$id} = 1; } if (length($id) >= $self->{_maxidlength}) { $self->{_maxidlength} = length($id); } if (length($fileid) >= $self->{_maxfileidlength}) { $self->{_maxfileidlength} = length($fileid); } if (length($pos) >= $self->{_maxposlength}) { $self->{_maxposlength} = length($pos); } if (length($length) >= $self->{_maxlengthlength}) { $self->{_maxlengthlength} = length($length); }
}
_index_filedescriptionprevnextTop
sub _index_file {
    my ($self,$file) = @_;

    open(FILE,"<$file") || $self->throw("Can't open file [$file]");

    my $recstart = 0;
    my $fileid = $self->get_fileid_by_filename($file);
    my $found = 0;
    my $id;
    my $count;

    my $primary       = $self->primary_pattern;
    my $start_pattern = $self->start_pattern;

    my $pos = 0;

    my $new_primary_entry;
    
    my $length;
    #my $pos = 0;
my $fh =\* FILE; my $done = -1; my @secondary_names = $self->secondary_namespaces; my %secondary_id; while (<$fh>) { if ($_ =~ /$start_pattern/) { if ($done == 0) { $id = $new_primary_entry; my $tmplen = tell($fh) - length($_); $length = $tmplen - $pos; if (!defined($id)) { $self->throw("No id defined for sequence"); } if (!defined($fileid)) { $self->throw("No fileid defined for file $file"); } if (!defined($pos)) { $self->throw("No position defined for " . $id . "\n"); } if (!defined($length)) { $self->throw("No length defined for " . $id . "\n"); } $self->_add_id_position($id,$pos,$fileid,$length,\%secondary_id); $pos = $tmplen; if ($count%1000 == 0) { print STDERR "Indexed $count ids\n"; } $count++; } else { $done = 0; } } if ($_ =~ /$primary/) { $new_primary_entry = $1; } my $secondary_patterns = $self->secondary_patterns; foreach my $sec (@secondary_names) { my $pattern = $secondary_patterns->{$sec}; if ($_ =~ /$pattern/) { $secondary_id{$sec} = $1; } } } # Remeber to add in the last one
$id = $new_primary_entry; my $tmplen = tell($fh) - length($_); $length = $tmplen - $pos; if (!defined($id)) { $self->throw("No id defined for sequence"); } if (!defined($fileid)) { $self->throw("No fileid defined for file $file"); } if (!defined($pos)) { $self->throw("No position defined for " . $id . "\n"); } if (!defined($length)) { $self->throw("No length defined for " . $id . "\n"); } $self->_add_id_position($id,$pos,$fileid,$length,\%secondary_id); close(FILE);
}
database_namedescriptionprevnextTop
sub database_name {
    my ($self,$arg) = @_;

    if (defined($arg)) {
	$self->{_database_name} = $arg;
    }
    return $self->{_database_name};
}
find_entrydescriptionprevnextTop
sub find_entry {
    my ($self,$fh,$start,$end,$id,$recsize) = @_;

    my $mid = int(($end+1+$start)/2);
my $pos = ($mid-1)*$recsize + $self->{_start_pos}; my ($record) = $self->read_record($fh,$pos,$recsize); my ($entryid,$rest) = split(/\t/,$record,2); # print "Mid $recsize $mid $pos:$entryid:$rest:$record\n";
# print "Entry :$id:$entryid:$rest\n";
my ($first,$second) = sort { $a cmp $b} ($id,$entryid); if ($id eq $entryid) { return ($id,$rest,$pos-$recsize); } elsif ($first eq $id) { if ($end-$start <= 1) { return; } my $end = $mid; # print "Moving up $entryid $id\n";
$self->find_entry($fh,$start,$end,$id,$recsize); } elsif ($second eq $id ) { # print "Moving down $entryid $id\n";
if ($end-$start <= 1) { return; } $start = $mid; $self->find_entry($fh,$start,$end,$id,$recsize); }
}
formatdescriptionprevnextTop
sub format {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'format'} = $value;
    }
    return $obj->{'format'};
}
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
    my ($self,$acc) = @_;

    if ($self->primary_namespace eq "ACC") {
       return $self->get_Seq_by_id($acc);
    } else {
      return $self->get_Seq_by_secondary("ACC",$acc);
    }
}
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
    my ($self,$id) = @_;
   
    my ($fh,$length) = $self->get_stream_by_id($id);
    
    if (!defined($self->format)) {
	$self->throw("Can't create sequence - format is not defined");
    }
   
    if(!$fh){
      return;
    }
    if (!defined($self->{_seqio})) {
     
	$self->{_seqio} = new Bio::SeqIO(-fh => $fh,
					 -format => $self->format);
    } else {
      
	$self->{_seqio}->fh($fh);
    }
    
    return $self->{_seqio}->next_seq;
}
get_Seq_by_secondarydescriptionprevnextTop
sub get_Seq_by_secondary {
    my ($self,$name,$id) = @_;

    my @names = $self->secondary_namespaces;

    my $found = 0;
    foreach my $tmpname (@names) {
	if ($name eq $tmpname) {
	    $found = 1;
	}
    }

    if ($found == 0) {
	$self->throw("Secondary index for $name doesn't exist\n");
    }

    my $fh = $self->open_secondary_index($name);

    syseof ($fh);

    my $filesize = systell($fh);

    my $recsize = $self->{_secondary_record_size}{$name};
#    print "Name " . $recsize . "\n";
my $end = ($filesize-$self->{_start_pos})/$recsize;
# print "End $end $filesize\n";
my ($newid,$primary_id,$pos) = $self->find_entry($fh,0,$end,$id,$recsize); sysseek($fh,$pos,0); # print "Found new id $newid $primary_id\n";
# We now need to shuffle up the index file to find the top secondary entry
my $record = $newid; while ($record =~ /^$newid/ && $pos >= 0) { $record = $self->read_record($fh,$pos,$recsize); $pos = $pos - $recsize; # print "Up record = $record:$newid\n";
} $pos += $recsize; # print "Top position is $pos\n";
# Now we have to shuffle back down again to read all the secondary entries
my $current_id = $newid; my %primary_id; $primary_id{$primary_id} = 1; while ($current_id eq $newid) { $record = $self->read_record($fh,$pos,$recsize); print "Record is :$record:\n"; my ($secid,$primary_id) = split(/\t/,$record,2); $current_id = $secid; if ($current_id eq $newid) { $primary_id =~ s/ //g; # print "Primary $primary_id\n";
$primary_id{$primary_id} = 1; $pos = $pos + $recsize; # print "Down record = $record\n";
} } if (!defined($newid)) { return; } my $entry; foreach my $id (keys %primary_id) { $entry .= $self->get_Seq_by_id($id); } return $entry;
}
get_entry_by_iddescriptionprevnextTop
sub get_entry_by_id {
    my ($self,$id) = @_;

    my ($fh,$length) = $self->get_stream_by_id($id);

    my $entry;

    sysread($fh,$entry,$length);

    return $entry;
}
get_filehandle_by_fileiddescriptionprevnextTop
sub get_filehandle_by_fileid {
    my ($self,$fileid) = @_;

    if (!defined($self->{_fileid}{$fileid})) {
	$self->throw("ERROR: undefined fileid in index [$fileid]");
    }
   
    return $self->{_fileid}{$fileid};
}
get_fileid_by_filenamedescriptionprevnextTop
sub get_fileid_by_filename {
    my ($self,$file) = @_;
    
    if (!defined($self->{_dbfile})) {
	$self->throw("No file to fileid mapping present.  Has the fileid file been read?");
    }

    
    return $self->{_dbfile}{$file};
}
get_stream_by_iddescriptionprevnextTop
sub get_stream_by_id {
    my ($self,$id) = @_;

    my $indexfh = $self->primary_index_filehandle;

    syseof ($indexfh);

    my $filesize = systell($indexfh);

    my $end = ($filesize-$self->{_start_pos})/$self->record_size;
my ($newid,$rest,$fhpos) = $self->find_entry($indexfh,0,$end,$id,$self->record_size); my ($fileid,$pos,$length) = split(/\t/,$rest); #print STDERR "OBDAIndex Found id entry $newid $fileid $pos $length:$rest\n";
if (!$newid) { return; } my $fh = $self->get_filehandle_by_fileid($fileid); my $file = $self->{_file}{$fileid}; open (IN,"<$file"); $fh =\* IN; my $entry; sysseek($fh,$pos,0); return ($fh,$length);
}
index_directorydescriptionprevnextTop
sub index_directory {
    my ($self,$arg) = @_;

    if (defined($arg)) {
	if ($arg !~ /\/$/) {
	    $arg .= "/";
	}
	$self->{_index_directory} = $arg;
    }
    return $self->{_index_directory};
}
index_typedescriptionprevnextTop
sub index_type {
    my ($self,$arg) = @_;

    if (defined($arg)) {
	$self->{_index_type} = $arg;
    }
    return $self->{_index_type};
}
index_versiondescriptionprevnextTop
sub index_version {
    my ($self,$arg) = @_;

    if (defined($arg)) {
	$self->{_index_version} = $arg;
    }
    return $self->{_index_version};
}
make_config_filedescriptionprevnextTop
sub make_config_file {
    my ($self,$files) = @_;
    
    my @files = @$files;

    my $dir = $self->index_directory;

    my $configfile = $dir . $self->database_name . "/" .CONFIG_FILE_NAME;

    open(CON,">$configfile") || $self->throw("Can't create config file [$configfile]");

    # First line must be the type of index - in this case flat
print CON "index\tflat/1\n"; # Now the fileids
my $count = 0; foreach my $file (@files) { my $size = -s $file; print CON "fileid_$count\t$file\t$size\n"; my $fh = new FileHandle("<$file"); $self->{_fileid}{$count} = $fh; $self->{_file} {$count} = $file; $self->{_dbfile}{$file} = $count; $self->{_size}{$count} = $size; $count++; } # Now the namespaces
print CON "primary_namespace\t" .$self->primary_namespace. "\n"; # Needs fixing for the secondary stuff
my $second_patterns = $self->secondary_patterns; my @second = keys %$second_patterns; if ((@second)) { print CON "secondary_namespaces"; foreach my $second (@second) { print CON "\t$second"; } print CON "\n"; } # Now the config format
if (!defined($self->format)) { $self->throw("Format does not exist in module - can't write config file"); } else { print CON "format\t" . $self->format . "\n"; } close(CON);
}
make_indexdescriptionprevnextTop
sub make_index {
    my ($self,$dbname,@files) = @_;;
    
    my $rootdir = $self->index_directory;

    if (!defined($rootdir)) {
	$self->throw("No index directory set - can't build indices");
    }
    
    if (! -d $rootdir) {
	$self->throw("Index directory [$rootdir] is not a directory. Cant' build indices");
    }
    if (!(@files)) {
	$self->throw("Must enter an array of filenames to index");
    }
    
    if (!defined($dbname)) {
	$self->throw("Must enter an index name for your files");
    }
    
    my $pwd = `pwd`; chomp($pwd);

    foreach my $file (@files) {
	if ($file !~ /^\//) {
	    $file = $pwd . "/$file";
	}
	if (! -e $file) {
	    $self->throw("Can't index file [$file] as it doesn't exist");
	}
    }
    
    $self->database_name($dbname);
    $self->make_indexdir($rootdir);;
    $self->make_config_file(\@files);
    
    # Finally lets index
foreach my $file (@files) { $self->_index_file($file); } # And finally write out the indices
$self->write_primary_index; $self->write_secondary_indices;
}
make_indexdirdescriptionprevnextTop
sub make_indexdir {
    my ($self,$rootdir) = @_;

    if (!defined($rootdir)) {
	$self->throw("Must enter an index directory name for make_indexdir");
    }
    if (! -e $rootdir) {
	$self->throw("Root index directory [$rootdir] doesn't exist");
    }

    if (! -d $rootdir) {
	$self->throw("[$rootdir] exists but is not a directory");
    }

    if ($rootdir !~ /\/$/) {
	$rootdir .= "/";
    }

    my $indexdir = $rootdir . $self->database_name;

    if (! -e $indexdir) {
	mkdir $indexdir,0755;
    } else {
	$self->throw("Index directory " . $indexdir . " already exists. Exiting\n");
    }
}
newdescriptionprevnextTop
sub new {
    my($class, @args) = @_;

    my $self = $class->SUPER::new(@args);

    bless $self, $class;

    my ($index_dir,$dbname,$format,$primary_pattern,$primary_namespace,
	$start_pattern,$secondary_patterns) =  
	    $self->_rearrange([qw(INDEX_DIR
				  DBNAME
				  FORMAT
				  PRIMARY_PATTERN
				  PRIMARY_NAMESPACE
				  START_PATTERN
				  SECONDARY_PATTERNS)], @args);
    
    $self->index_directory($index_dir);
    $self->database_name     ($dbname);

    if ($self->index_directory && $dbname) {

	$self->read_config_file;
	
	my $fh = $self->primary_index_filehandle;
        my $record_width = $self->read_header($fh);

        $self->record_size($record_width);
    }


    $self->format            ($format);
    $self->primary_pattern   ($primary_pattern);
    $self->primary_namespace ($primary_namespace);
    $self->start_pattern     ($start_pattern);
    $self->secondary_patterns($secondary_patterns);

    return $self;
}
new_EMBL_indexdescriptionprevnextTop
sub new_EMBL_index {
   my ($self,$index_dir,$dbname,@files) = @_;
   
   my %secondary_patterns;

   my $start_pattern = "^ID   (\\S+)";
   my $primary_pattern = "^AC   (\\S+)\\;";
   my $primary_namespace = "ACC";

   $secondary_patterns{"ID"} = $start_pattern;

   my $index = new Bio::DB::Flat::OBDAIndex(-index_dir          => $index_dir,
					    -format             => 'embl',
					    -primary_pattern    => $primary_pattern,
					    -primary_namespace  => "ACC",
					    -start_pattern      => $start_pattern,
					    -secondary_patterns =>\% secondary_patterns);
   
    $index->make_index($dbname,@files);

   return $index;
}
new_FASTA_indexdescriptionprevnextTop
sub new_FASTA_index {
   my ($self,$index_dir,$dbname,@files) =  @_;

   my %secondary_patterns;

   my $start_pattern = "^>";
   my $primary_pattern = "^>(\\S+)";
   my $primary_namespace = "ACC"; 

   $secondary_patterns{"ID"} = "^>\\S+ +(\\S+)";

   my $index =  new Bio::DB::Flat::OBDAIndex(-index_dir          => $index_dir,
					     -format             => 'fasta',
					     -primary_pattern    => $primary_pattern,
					     -primary_namespace  => "ACC",
					     -start_pattern      => $start_pattern,
					     -secondary_patterns =>\% secondary_patterns);
   
   $index->make_index($dbname,@files);

   return $index;

}



1;
}
new_SWISSPROT_indexdescriptionprevnextTop
sub new_SWISSPROT_index {
    my ($self,$index_dir,$dbname,@files) = @_;
    
    my %secondary_patterns;
    
    my $start_pattern = "^ID   (\\S+)";
    my $primary_pattern = "^AC   (\\S+)\\;";
    
    $secondary_patterns{"ID"} = $start_pattern;

    my $index =  new Bio::DB::Flat::OBDAIndex(-index_dir          => $index_dir,
					      -format             => 'swiss',
					      -primary_pattern    => $primary_pattern,
					      -primary_namespace  => "ACC",
					      -start_pattern      => $start_pattern,
					      -secondary_patterns =>\% secondary_patterns);
    
    $index->make_index($dbname,@files);
}
new_from_registrydescriptionprevnextTop
sub new_from_registry {
    my ($self,%config) =  @_;
   
    my $dbname   = $config{'dbname'};
    my $location = $config{'location'};
    
    my $index =  new Bio::DB::Flat::OBDAIndex(-dbname    => $dbname,
					      -index_dir => $location,
					      );
}
new_secondary_filehandledescriptionprevnextTop
sub new_secondary_filehandle {
    my ($self,$name) = @_;

    my $indexdir = $self->index_directory;

    my $secindex = $indexdir . $self->database_name . "/id_$name.index";

    my $fh = new FileHandle(">$secindex");

    return $fh;
}
open_secondary_indexdescriptionprevnextTop
sub open_secondary_index {
    my ($self,$name) = @_;

    if (!defined($self->{_secondary_filehandle}{$name})) {

	my $indexdir = $self->index_directory;
	my $secindex = $indexdir . $self->database_name . "/id_$name.index";
	
	if (! -e $secindex) {
	    $self->throw("Index is not present for namespace [$name]\n");
	}

        my $newfh  = new FileHandle("<$secindex");
	my $reclen = $self->read_header($newfh);

	$self->{_secondary_filehandle} {$name} = $newfh;
	$self->{_secondary_record_size}{$name} = $reclen;
    }

    return $self->{_secondary_filehandle}{$name};
}
primary_index_filedescriptionprevnextTop
sub primary_index_file {
    my ($self) = @_;

    return $self->index_directory . $self->database_name . "/key_" . $self->primary_namespace . ".key";
}
primary_index_filehandledescriptionprevnextTop
sub primary_index_filehandle {
    my ($self) = @_;

    if (!defined ($self->{_primary_index_handle})) {
	$self->{_primary_index_handle} = new FileHandle("<" . $self->primary_index_file);
    }
    return $self->{_primary_index_handle};
}
primary_namespacedescriptionprevnextTop
sub primary_namespace {
  my ($self,$arg) =  @_;

  if (defined($arg)) {
    $self->{_primary_namespace} =  $arg;
  }
  return $self->{_primary_namespace};
}
primary_patterndescriptionprevnextTop
sub primary_pattern {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'primary_pattern'} = $value;
    }

    return $obj->{'primary_pattern'};
}
read_config_filedescriptionprevnextTop
sub read_config_file {
    my ($self) = @_;

    my $dir = $self->index_directory . $self->database_name . "/";;

    if (! -d $dir) {
	$self->throw("No index directory [" . $dir  . "]. Can't read ".  CONFIG_FILE_NAME);
    }
    
    my $configfile = $dir . CONFIG_FILE_NAME;
    
    if (! -e $configfile) {
	$self->throw("No config file [$configfile]. Can't read namespace");
    }
    
    open(CON,"<$configfile") || $self->throw("Can't open configfile [$configfile]");

    # First line must be type
my $line = <CON>; chomp($line); my $version; # This is hard coded as we only index flatfiles here
if ($line =~ /index\tflat\/(\d+)/) { $version = $1; } else { $self->throw("First line not compatible with flat file index. Should be something like\n\nindex\tflat/1"); } $self->index_type("flat"); $self->index_version($version); while (<CON>) { chomp; # Look for fileid lines
if ($_ =~ /^fileid_(\d+)\t(\S+)\t(\d+)/) { my $fileid = $1; my $filename = $2; my $filesize = $3; if (! -e $filename) { $self->throw("File [$filename] does not exist!"); } if (-s $filename != $filesize) { $self->throw("Flatfile size for $filename differs from what the index thinks it is. Real size [" . (-s $filename) . "] Index thinks it is [" . $filesize . "]"); } my $fh = new FileHandle("<$filename"); $self->{_fileid}{$fileid} = $fh; $self->{_file} {$fileid} = $filename; $self->{_dbfile}{$filename} = $fileid; $self->{_size} {$fileid} = $filesize; } # Look for namespace lines
if ($_ =~ /(.*)_namespace.*\t(\S+)/) { if ($1 eq "primary") { $self->primary_namespace($2); } elsif ($1 eq "secondary") { $self->secondary_namespaces($2); } else { $self->throw("Unknown namespace name in config file [$1"); } } # Look for format lines
if ($_ =~ /format\t(\S+)/) { # Check the format here?
$self->format($1); } } close(CON); # Now check we have all that we need
my @fileid_keys = keys (%{$self->{_fileid}}); if (!(@fileid_keys)) { $self->throw("No flatfile fileid files in config - check the index has been made correctly"); } if (!defined($self->primary_namespace)) { $self->throw("No primary namespace exists"); } if (! -e $self->primary_index_file) { $self->throw("Primary index file [" . $self->primary_index_file . "] doesn't exist"); }
}
read_headerdescriptionprevnextTop
sub read_header {
    my ($self,$fh) = @_;

    my $record_width;

    sysread($fh,$record_width,HEADER_SIZE);

    $self->{_start_pos} = HEADER_SIZE;
    $record_width =~ s/ //g;
    $record_width = $record_width * 1;

    return $record_width;
}
read_recorddescriptionprevnextTop
sub read_record {
  my ($self,$fh,$pos,$len) = @_;

  sysseek($fh,$pos,0);

  my $record;
    
  sysread($fh,$record,$len);

  return $record;
}
record_sizedescriptionprevnextTop
sub record_size {
    my ($self,$arg) = @_;

    if (defined($arg)) {
      $self->{_record_size} = $arg;
    }
    return $self->{_record_size};
}
secondary_namespacesdescriptionprevnextTop
sub secondary_namespaces {
   my ($obj,$value) = @_;

   if (!defined($obj->{secondary_namespaces})) {
       $obj->{secondary_namespaces} = [];
   }
   if( defined $value) {
       push(@{$obj->{'secondary_namespaces'}},$value);
    }
   return @{$obj->{'secondary_namespaces'}};

}



## These are indexing routines to index commonly used format - fasta
## swissprot and embl
}
secondary_patternsdescriptionprevnextTop
sub secondary_patterns {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'secondary_patterns'} = $value;

      my @names = keys %$value;

      foreach my $name (@names) {
	  $obj->secondary_namespaces($name);
      }
    }
    return $obj->{'secondary_patterns'};
}
start_patterndescriptionprevnextTop
sub start_pattern {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'start_pattern'} = $value;
    }
    return $obj->{'start_pattern'};
}
syseofdescriptionprevnextTop
sub syseof {
sysseek($_[0], 0, SEEK_END)
}
systelldescriptionprevnextTop
sub systell {
sysseek($_[0], 0, SEEK_CUR)
}
write_primary_indexdescriptionprevnextTop
sub write_primary_index {
    my ($self) = @_;

    my @ids = keys %{$self->{_id}};

    @ids = sort {$a cmp $b} @ids;

    print STDERR "Number of ids = " . scalar(@ids) . "\n";

    open (INDEX,">" . $self->primary_index_file) || $self->throw("Can't open primary index file [" . $self->primary_index_file . "]");

    my $recordlength = $self->{_maxidlength} +
	               $self->{_maxfileidlength} + 
	               $self->{_maxposlength} +
   		       $self->{_maxlengthlength} + 3;
	
    
    print INDEX sprintf("%4d",$recordlength);

    foreach my $id (@ids) {

	if (!defined($self->{_id}{$id}{_fileid})) {
	    $self->throw("No fileid for $id\n");
	}
	if (!defined($self->{_id}{$id}{_pos})) {
	    $self->throw("No position for $id\n");
	}
	if (!defined($self->{_id}{$id}{_length})) {
	    $self->throw("No length for $id");
	}

	my $record =  $id              . "\t" . 
	    $self->{_id}{$id}{_fileid} . "\t" .
	    $self->{_id}{$id}{_pos}    . "\t" .
	    $self->{_id}{$id}{_length};

	print INDEX sprintf("%-${recordlength}s",$record);

    }
    close(INDEX);
}
write_secondary_indicesdescriptionprevnextTop
sub write_secondary_indices {
    my ($self) = @_;

    # These are the different 
my @names = keys (%{$self->{_secondary_id}}); foreach my $name (@names) { my @seconds = keys %{$self->{_secondary_id}{$name}}; # First we need to loop over to get the longest record.
my $length = 0; foreach my $second (@seconds) { my $tmplen = length($second) + 1; my @prims = keys %{$self->{_secondary_id}{$name}{$second}}; foreach my $prim (@prims) { my $recordlen = $tmplen + length($prim); if ($recordlen > $length) { $length = $recordlen; } } } # Now we can print the index
my $fh = $self->new_secondary_filehandle($name); print $fh sprintf("%4d",$length); @seconds = sort @seconds; foreach my $second (@seconds) { my @prims = keys %{$self->{_secondary_id}{$name}{$second}}; my $tmp = $second; foreach my $prim (@prims) { my $record = $tmp . "\t" . $prim; if (length($record) > $length) { $self->throw("Something has gone horribly wrong - length of record is more than we thought [$length]\n"); } else { print $fh sprintf("%-${length}s",$record); print $fh sprintf("%-${length}s",$record); } } } close($fh); }
}
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 one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org             - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHOR - Michele ClampTop
Email - michele@sanger.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with an "_" (underscore).