#
# BioPerl module for Bio::DB::Flat::BinarySearch
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Michele Clamp <michele@sanger.ac.uk>>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files
=head1 SYNOPSIS
TODO: SYNOPSIS NEEDED!
=head1 DESCRIPTION
This module can be used both to index sequence files and also to
retrieve sequences from existing sequence files.
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 L<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.
=head2 Index creation
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 E<gt> and the
primary key is all characters up to the first space after the E<gt>
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 = Bio::DB::Flat::BinarySearch->new(
-directory => "/home/max/",
-dbname => "mydb",
-start_pattern => $start_pattern,
-primary_pattern => $primary_pattern,
-primary_namespace => "ID",
-format => "fasta" );
my @files = ("file1","file2","file3");
$index->build_index(@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 DB_File indexer, BDB.
The formats currently supported by this module are fasta, Swissprot,
and EMBL.
=head2 Creating indices with secondary keys
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 = Bio::DB::Flat::BinarySearch->new(
-directory => $index_directory,
-dbname => "ppp",
-write_flag => 1,
-verbose => 1,
-start_pattern => $start_pattern,
-primary_pattern => $primary_pattern,
-primary_namespace => 'AC',
-secondary_patterns => \%secondary_patterns);
$index->build_index($seqfile);
Of course having secondary indices makes indexing slower and use more
memory.
=head2 Index reading
To fetch sequences using an existing index first of all create your sequence
object
my $index = Bio::DB::Flat::BinarySearch->new(
-directory => $index_directory);
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 = Bio::SeqIO->new(-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
$index->secondary_namespaces("ID");
Then the following call can be used
my $seq = $index->get_Seq_by_secondary('ID','1433_CAEEL');
These calls are not yet implemented
my $fh = $index->get_stream_by_secondary('ID','1433_CAEEL');
my $entry = $index->get_entry_by_secondary('ID','1433_CAEEL');
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Michele Clamp
Email - michele@sanger.ac.uk
=head1 CONTRIBUTORS
Jason Stajich, jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with an "_" (underscore).
=cut
package Bio::DB::Flat::BinarySearch;
use strict;
use Fcntl qw(SEEK_END SEEK_CUR);
# rather than using tell which might be buffered
sub systell { sysseek( $_[0], 0, SEEK_CUR ) }
sub syseof { sysseek( $_[0], 0, SEEK_END ) }
use File::Spec;
use Bio::Root::RootI;
use Bio::SeqIO;
use Bio::Seq;
use base qw(Bio::DB::RandomAccessI);
use constant CONFIG_FILE_NAME => 'config.dat';
use constant HEADER_SIZE => 4;
use constant DEFAULT_FORMAT => 'fasta';
my @formats = [ 'FASTA', 'SWISSPROT', 'EMBL' ];
=head2 new
Title : new
Usage : For reading
my $index = Bio::DB::Flat::BinarySearch->new(
-directory => '/Users/michele/indices/dbest',
-dbname => 'mydb',
-format => 'fasta');
For writing
my %secondary_patterns = {"ACC" => "^>\\S+ +(\\S+)"}
my $index = Bio::DB::Flat::BinarySearch->new(
-directory => '/Users/michele/indices',
-dbname => 'mydb',
-primary_pattern => "^>(\\S+)",
-secondary_patterns => \%secondary_patterns,
-primary_namespace => "ID");
my @files = ('file1','file2','file3');
$index->build_index(@files);
Function: create a new Bio::DB::Flat::BinarySearch object
Returns : new Bio::DB::Flat::BinarySearch
Args : -directory Root directory for index files
-dbname Name of subdirectory containing indices
for named database
-write_flag Allow building index
-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
=cut
sub new {
my ( $class, @args ) = @_;
my $self = $class->SUPER::new(@args);
bless $self, $class;
my ( $index_dir, $dbname, $format, $write_flag, $primary_pattern,
$primary_namespace, $start_pattern, $secondary_patterns )
= $self->_rearrange(
[
qw(DIRECTORY
DBNAME
FORMAT
WRITE_FLAG
PRIMARY_PATTERN
PRIMARY_NAMESPACE
START_PATTERN
SECONDARY_PATTERNS)
],
@args
);
$self->index_directory($index_dir);
$self->dbname($dbname);
if ( $self->index_directory && $self->read_config_file ) {
my $fh = $self->primary_index_filehandle;
my $record_width = $self->read_header($fh);
$self->record_size($record_width);
}
$format ||= DEFAULT_FORMAT;
$self->format($format);
$self->write_flag($write_flag);
if ( $self->write_flag && !$primary_namespace ) {
(
$primary_namespace, $primary_pattern,
$start_pattern, $secondary_patterns
) = $self->_guess_patterns( $self->format );
}
$self->primary_pattern($primary_pattern);
$self->primary_namespace($primary_namespace);
$self->start_pattern($start_pattern);
$self->secondary_patterns($secondary_patterns);
return $self;
}
sub new_from_registry {
my ( $self, %config ) = @_;
my $dbname = $config{'dbname'};
my $location = $config{'location'};
my $index = Bio::DB::Flat::BinarySearch->new(
-dbname => $dbname,
-index_dir => $location,
);
}
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $obj->get_Seq_by_id($newval)
Function:
Example :
Returns : value of get_Seq_by_id
Args : newvalue (optional)
=cut
sub get_Seq_by_id {
my ( $self, $id ) = @_;
# too many uninit variables...
local $^W = 0;
my ( $fh, $length ) = $self->get_stream_by_id($id);
unless ( defined( $self->format ) ) {
$self->throw("Can't create sequence - format is not defined");
}
return unless $fh;
unless ( defined( $self->{_seqio} ) ) {
$self->{_seqio} = Bio::SeqIO->new(
-fh => $fh,
-format => $self->format
);
}
else {
$self->{_seqio}->_fh($fh);
}
return $self->{_seqio}->next_seq;
}
=head2 get_entry_by_id
Title : get_entry_by_id
Usage : $obj->get_entry_by_id($newval)
Function: Get a Bio::SeqI object for a unique ID
Returns : Bio::SeqI
Args : string
=cut
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;
}
=head2 get_stream_by_id
Title : get_stream_by_id
Usage : $obj->get_stream_by_id($id)
Function: Gets a Sequence stream for an id
Returns : Bio::SeqIO stream
Args : Id to lookup by
=cut
sub get_stream_by_id {
my ( $self, $id ) = @_;
unless ( $self->record_size ) {
if ( $self->index_directory && $self->read_config_file ) {
my $fh = $self->primary_index_filehandle;
my $record_width = $self->read_header($fh);
$self->record_size($record_width);
}
}
my $indexfh = $self->primary_index_filehandle;
syseof($indexfh);
my $filesize = systell($indexfh);
$self->throw("file was not parsed properly, record size is empty")
unless $self->record_size;
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 "BinarySearch Found id entry $newid $fileid $pos $length:$rest\n";
if ( !$newid ) {
return;
}
my $file = $self->{_file}{$fileid};
open my $IN, '<', $file or $self->throw("Could not read file '$file': $!");
my $entry;
sysseek( $IN, $pos, 0 );
return ( $IN, $length );
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $obj->get_Seq_by_acc($acc)
Function: Gets a Bio::SeqI object by accession number
Returns : Bio::SeqI object
Args : string representing accession number
=cut
sub get_Seq_by_acc {
my ( $self, $acc ) = @_;
# too many uninit variables...
local $^W = 0;
if ( $self->primary_namespace eq "ACC" ) {
return $self->get_Seq_by_id($acc);
}
else {
return $self->get_Seq_by_secondary( "ACC", $acc );
}
}
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $obj->get_Seq_by_version($version)
Function: Gets a Bio::SeqI object by accession.version number
Returns : Bio::SeqI object
Args : string representing accession.version number
=cut
sub get_Seq_by_version {
my ( $self, $acc ) = @_;
# too many uninit variables...
local $^W = 0;
if ( $self->primary_namespace eq "VERSION" ) {
return $self->get_Seq_by_id($acc);
}
else {
return $self->get_Seq_by_secondary( "VERSION", $acc );
}
}
=head2 get_Seq_by_secondary
Title : get_Seq_by_secondary
Usage : $obj->get_Seq_by_secondary($namespace,$acc)
Function: Gets a Bio::SeqI object looking up secondary accessions
Returns : Bio::SeqI object
Args : namespace name to check secondary namespace and an id
=cut
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 ) {
push @entry, $self->get_Seq_by_id($id);
}
return wantarray ? @entry : $entry[0];
}
=head2 read_header
Title : read_header
Usage : $obj->read_header($fhl)
Function: Reads the header from the db file
Returns : width of a record
Args : filehandle
=cut
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;
}
=head2 read_record
Title : read_record
Usage : $obj->read_record($fh,$pos,$len)
Function: Reads a record from a filehandle
Returns : String
Args : filehandle, offset, and length
=cut
sub read_record {
my ( $self, $fh, $pos, $len ) = @_;
sysseek( $fh, $pos, 0 );
my $record;
sysread( $fh, $record, $len );
return $record;
}
=head2 get_all_primary_ids
Title : get_all_primary_ids
Usage : @ids = $seqdb->get_all_primary_ids()
Function: gives an array of all the primary_ids of the
sequence objects in the database.
Returns : an array of strings
Args : none
=cut
sub get_all_primary_ids {
my $self = shift;
my $fh = $self->primary_index_filehandle;
syseof($fh);
my $filesize = systell($fh);
my $recsize = $self->record_size;
my $end = $filesize;
my @ids;
for ( my $pos = $self->{'_start_pos'} ; $pos < $end ; $pos += $recsize ) {
my $record = $self->read_record( $fh, $pos, $recsize );
my ($entryid) = split( /\t/, $record );
push @ids, $entryid;
}
@ids;
}
=head2 find_entry
Title : find_entry
Usage : $obj->find_entry($fh,$start,$end,$id,$recsize)
Function: Extract an entry based on the start,end,id and record size
Returns : string
Args : filehandle, start, end, id, recordsize
=cut
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 );
$rest =~ s/\s+$//;
# print "Mid $recsize $mid $pos:$entryid:$rest:$record\n";
# print "Entry :$id:$entryid:$rest\n";
my ( $first, $second ) =
$id le $entryid ? ( $id, $entryid ) : ( $entryid, $id );
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 );
}
}
=head2 build_index
Title : build_index
Usage : $obj->build_index(@files)
Function: Build the index based on a set of files
Returns : count of the number of entries
Args : List of filenames
=cut
sub build_index {
my ( $self, @files ) = @_;
$self->write_flag
or $self->throw('Cannot build index unless -write_flag is true');
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"
);
}
my $dbpath = File::Spec->catfile( $rootdir, $self->dbname );
if ( !-d $dbpath ) {
warn "Creating directory $dbpath\n";
mkdir $dbpath, 0777 or $self->throw("Couldn't create $dbpath: $!");
}
unless (@files) {
$self->throw("Must enter an array of filenames to index");
}
foreach my $file (@files) {
$file = File::Spec->rel2abs($file)
unless File::Spec->file_name_is_absolute($file);
unless ( -e $file ) {
$self->throw("Can't index file [$file] as it doesn't exist");
}
}
if ( my $filehash = $self->{_dbfile} ) {
push @files, keys %$filehash;
}
my %seen;
@files = grep { !$seen{$_}++ } @files;
# Lets index
$self->make_config_file( \@files );
my $entries = 0;
foreach my $file (@files) {
$entries += $self->_index_file($file);
}
# update alphabet if necessary
$self->make_config_file( \@files );
# And finally write out the indices
$self->write_primary_index;
$self->write_secondary_indices;
$entries;
}
=head2 _index_file
Title : _index_file
Usage : $obj->_index_file($newval)
Function:
Example :
Returns : value of _index_file
Args : newvalue (optional)
=cut
sub _index_file {
my ( $self, $file ) = @_;
my $v = $self->verbose;
open my $FILE, '<', $file or $self->throw("Could not read file '$file': $!");
my $recstart = 0;
my $fileid = $self->get_fileid_by_filename($file);
my $found = 0;
my $id;
my $count = 0;
my $primary = $self->primary_pattern;
my $start_pattern = $self->start_pattern;
my $pos = 0;
my $new_primary_entry;
my $length;
my $fh = $FILE;
my $done = -1;
my @secondary_names = $self->secondary_namespaces;
my %secondary_id;
my $last_one;
# In Windows, text files have '\r\n' as line separator, but when reading in
# text mode Perl will only show the '\n'. This means that for a line "ABC\r\n",
# "length $_" will report 4 although the line is 5 bytes in length.
# We assume that all lines have the same line separator and only read current line.
my $init_pos = tell($fh);
my $curr_line = <$fh>;
my $pos_diff = tell($fh) - $init_pos;
my $correction = $pos_diff - length $curr_line;
seek $fh, $init_pos, 0; # Rewind position to proceed to read the file
while (<$fh>) {
$last_one = $_;
$self->{alphabet} ||= $self->guess_alphabet($_);
if ( $_ =~ /$start_pattern/ ) {
if ( $done == 0 ) {
$id = $new_primary_entry;
$self->{alphabet} ||= $self->guess_alphabet($_);
my $tmplen = ( tell $fh ) - length($_) - $correction;
$length = $tmplen - $pos;
unless ( defined($id) ) {
$self->throw("No id defined for sequence");
}
unless ( defined($fileid) ) {
$self->throw("No fileid defined for file $file");
}
unless ( defined($pos) ) {
$self->throw( "No position defined for " . $id . "\n" );
}
unless ( defined($length) ) {
$self->throw( "No length defined for " . $id . "\n" );
}
$self->_add_id_position( $id, $pos, $fileid, $length,
\%secondary_id );
$pos = $tmplen;
if ( $count > 0 && $count % 1000 == 0 ) {
$self->debug("Indexed $count ids\n") if $v > 0;
}
$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;
}
}
}
# Remember to add in the last one
$id = $new_primary_entry;
# my $tmplen = (tell $fh) - length($last_one);
my $tmplen = ( tell $fh );
$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 );
$count++;
close $FILE;
$count;
}
=head2 write_primary_index
Title : write_primary_index
Usage : $obj->write_primary_index($newval)
Function:
Example :
Returns : value of write_primary_index
Args : newvalue (optional)
=cut
sub write_primary_index {
my ($self) = @_;
my @ids = keys %{ $self->{_id} };
@ids = sort { $a cmp $b } @ids;
open my $INDEX, '>', $self->primary_index_file
or $self->throw(
"Could not write primary index file '" . $self->primary_index_file . "': $!" );
my $recordlength =
$self->{_maxidlength} +
$self->{_maxfileidlength} +
$self->{_maxposlength} +
$self->{_maxlengthlength} + 3;
print $INDEX sprintf( "%04d", $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 );
}
}
=head2 write_secondary_indices
Title : write_secondary_indices
Usage : $obj->write_secondary_indices($newval)
Function:
Example :
Returns : value of write_secondary_indices
Args : newvalue (optional)
=cut
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( "%04d", $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", $record );
}
}
}
close($fh);
}
}
=head2 new_secondary_filehandle
Title : new_secondary_filehandle
Usage : $obj->new_secondary_filehandle($newval)
Function:
Example :
Returns : value of new_secondary_filehandle
Args : newvalue (optional)
=cut
sub new_secondary_filehandle {
my ( $self, $name ) = @_;
my $indexdir = $self->_config_path;
my $secindex = File::Spec->catfile( $indexdir, "id_$name.index" );
open my $fh, '>', $secindex or $self->throw("Could not write file '$secindex': $!");
return $fh;
}
=head2 open_secondary_index
Title : open_secondary_index
Usage : $obj->open_secondary_index($newval)
Function:
Example :
Returns : value of open_secondary_index
Args : newvalue (optional)
=cut
sub open_secondary_index {
my ( $self, $name ) = @_;
if ( !defined( $self->{_secondary_filehandle}{$name} ) ) {
my $indexdir = $self->_config_path;
my $secindex = $indexdir . "/id_$name.index";
if ( !-e $secindex ) {
$self->throw("Index is not present for namespace [$name]\n");
}
open my $newfh, '<', $secindex or $self->throw("Could not read file '$secindex': $!");
my $reclen = $self->read_header($newfh);
$self->{_secondary_filehandle}{$name} = $newfh;
$self->{_secondary_record_size}{$name} = $reclen;
}
return $self->{_secondary_filehandle}{$name};
}
=head2 _add_id_position
Title : _add_id_position
Usage : $obj->_add_id_position($newval)
Function:
Example :
Returns : value of _add_id_position
Args : newvalue (optional)
=cut
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) ) {
$self->throw("No position defined. Can't add id position");
}
if ( !defined($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;
}
$self->{_maxidlength} = length($id)
if !exists $self->{_maxidlength}
or length($id) >= $self->{_maxidlength};
$self->{_maxfileidlength} = length($fileid)
if !exists $self->{_maxfileidlength}
or length($fileid) >= $self->{_maxfileidlength};
$self->{_maxposlength} = length($pos)
if !exists $self->{_maxposlength}
or length($pos) >= $self->{_maxposlength};
$self->{_maxlengthlength} = length($length)
if !exists $self->{_maxlengthlength}
or length($length) >= $self->{_maxlengthlength};
}
=head2 make_config_file
Title : make_config_file
Usage : $obj->make_config_file($newval)
Function:
Example :
Returns : value of make_config_file
Args : newvalue (optional)
=cut
sub make_config_file {
my ( $self, $files ) = @_;
my @files = @$files;
my $configfile = $self->_config_file;
open my $CON, '>', $configfile
or $self->throw("Could not write config file '$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";
$self->{_file}{$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
unless ( defined( $self->format ) ) {
$self->throw(
"Format does not exist in module - can't write config file");
}
else {
my $format = $self->format;
my $alphabet = $self->alphabet;
my $alpha = $alphabet ? "/$alphabet" : '';
print $CON "format\t" . "$format\n";
}
close $CON;
}
=head2 read_config_file
Title : read_config_file
Usage : $obj->read_config_file($newval)
Function:
Example :
Returns : value of read_config_file
Args : newvalue (optional)
=cut
sub read_config_file {
my ($self) = @_;
my $configfile = $self->_config_file;
return unless -e $configfile;
open my $CON, '<', $configfile
or $self->throw("Could not read config file '$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 =~ m{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(.+)\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
. "]" );
}
$self->{_file}{$fileid} = $filename;
$self->{_dbfile}{$filename} = $fileid;
$self->{_size}{$fileid} = $filesize;
}
# Look for namespace lines
if (/(.*)_namespaces?\t(.+)/) {
if ( $1 eq "primary" ) {
$self->primary_namespace($2);
}
elsif ( $1 eq "secondary" ) {
$self->secondary_namespaces( split "\t", $2 );
}
else {
$self->throw("Unknown namespace name in config file [$1");
}
}
# Look for format lines
if ( $_ =~ /format\t(\S+)/ ) {
# Check the format here?
my $format = $1;
# handle LSID format
if ( $format =~ /^URN:LSID:open-bio\.org:(\w+)(?:\/(\w+))?/ ) {
$self->format($1);
$self->alphabet($2);
}
else { # compatibility with older versions
$self->format($1);
}
}
}
close($CON);
# Now check we have all that we need
my @fileid_keys = keys( %{ $self->{_file} } );
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" );
}
1;
}
=head2 get_fileid_by_filename
Title : get_fileid_by_filename
Usage : $obj->get_fileid_by_filename($newval)
Function:
Example :
Returns : value of get_fileid_by_filename
Args : newvalue (optional)
=cut
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};
}
=head2 get_filehandle_by_fileid
Title : get_filehandle_by_fileid
Usage : $obj->get_filehandle_by_fileid($newval)
Function:
Example :
Returns : value of get_filehandle_by_fileid
Args : newvalue (optional)
=cut
sub get_filehandle_by_fileid {
my ( $self, $fileid ) = @_;
if ( !defined( $self->{_file}{$fileid} ) ) {
$self->throw("ERROR: undefined fileid in index [$fileid]");
}
open my $fh, '<', $self->{_file}{$fileid} or $self->throw("Could not read file '$self->{_file}{$fileid}': $!");
return $fh;
}
=head2 primary_index_file
Title : primary_index_file
Usage : $obj->primary_index_file($newval)
Function:
Example :
Returns : value of primary_index_file
Args : newvalue (optional)
=cut
sub primary_index_file {
my ($self) = @_;
return File::Spec->catfile( $self->_config_path,
"key_" . $self->primary_namespace . ".key" );
}
=head2 primary_index_filehandle
Title : primary_index_filehandle
Usage : $obj->primary_index_filehandle($newval)
Function:
Example :
Returns : value of primary_index_filehandle
Args : newvalue (optional)
=cut
sub primary_index_filehandle {
my ($self) = @_;
unless ( defined( $self->{'_primary_index_handle'} ) ) {
my $primary_file = $self->primary_index_file;
open $self->{'_primary_index_handle'}, '<', $primary_file
or self->throw("Could not read file '$primary_file': $!\n");
}
return $self->{'_primary_index_handle'};
}
=head2 format
Title : format
Usage : $obj->format($newval)
Function:
Example :
Returns : value of format
Args : newvalue (optional)
=cut
sub format {
my ( $obj, $value ) = @_;
if ( defined $value ) {
$obj->{'format'} = $value;
}
return $obj->{'format'};
}
sub alphabet {
my ( $obj, $value ) = @_;
if ( defined $value ) {
$obj->{alphabet} = $value;
}
return $obj->{alphabet};
}
=head2 write_flag
Title : write_flag
Usage : $obj->write_flag($newval)
Function:
Example :
Returns : value of write_flag
Args : newvalue (optional)
=cut
sub write_flag {
my ( $obj, $value ) = @_;
if ( defined $value ) {
$obj->{'write_flag'} = $value;
}
return $obj->{'write_flag'};
}
=head2 dbname
Title : dbname
Usage : $obj->dbname($newval)
Function: get/set database name
Example :
Returns : value of dbname
Args : newvalue (optional)
=cut
sub dbname {
my $self = shift;
my $d = $self->{flat_dbname};
$self->{flat_dbname} = shift if @_;
$d;
}
=head2 index_directory
Title : index_directory
Usage : $obj->index_directory($newval)
Function:
Example :
Returns : value of index_directory
Args : newvalue (optional)
=cut
sub index_directory {
my ( $self, $arg ) = @_;
if ( defined($arg) ) {
if ( $arg !~ m{/$} ) {
$arg .= "/";
}
$self->{_index_directory} = $arg;
}
return $self->{_index_directory};
}
sub _config_path {
my $self = shift;
my $root = $self->index_directory;
my $dbname = $self->dbname;
File::Spec->catfile( $root, $dbname );
}
sub _config_file {
my $self = shift;
my $path = $self->_config_path;
File::Spec->catfile( $path, CONFIG_FILE_NAME );
}
=head2 record_size
Title : record_size
Usage : $obj->record_size($newval)
Function:
Example :
Returns : value of record_size
Args : newvalue (optional)
=cut
sub record_size {
my $self = shift;
$self->{_record_size} = shift if @_;
return $self->{_record_size};
}
=head2 primary_namespace
Title : primary_namespace
Usage : $obj->primary_namespace($newval)
Function:
Example :
Returns : value of primary_namespace
Args : newvalue (optional)
=cut
sub primary_namespace {
my $self = shift;
$self->{_primary_namespace} = shift if @_;
return $self->{_primary_namespace};
}
=head2 index_type
Title : index_type
Usage : $obj->index_type($newval)
Function:
Example :
Returns : value of index_type
Args : newvalue (optional)
=cut
sub index_type {
my $self = shift;
$self->{_index_type} = shift if @_;
return $self->{_index_type};
}
=head2 index_version
Title : index_version
Usage : $obj->index_version($newval)
Function:
Example :
Returns : value of index_version
Args : newvalue (optional)
=cut
sub index_version {
my $self = shift;
$self->{_index_version} = shift if @_;
return $self->{_index_version};
}
=head2 primary_pattern
Title : primary_pattern
Usage : $obj->primary_pattern($newval)
Function:
Example :
Returns : value of primary_pattern
Args : newvalue (optional)
=cut
sub primary_pattern {
my $obj = shift;
$obj->{'primary_pattern'} = shift if @_;
return $obj->{'primary_pattern'};
}
=head2 start_pattern
Title : start_pattern
Usage : $obj->start_pattern($newval)
Function:
Example :
Returns : value of start_pattern
Args : newvalue (optional)
=cut
sub start_pattern {
my $obj = shift;
$obj->{'start_pattern'} = shift if @_;
return $obj->{'start_pattern'};
}
=head2 secondary_patterns
Title : secondary_patterns
Usage : $obj->secondary_patterns($newval)
Function:
Example :
Returns : value of secondary_patterns
Args : newvalue (optional)
=cut
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'};
}
=head2 secondary_namespaces
Title : secondary_namespaces
Usage : $obj->secondary_namespaces($newval)
Function:
Example :
Returns : value of secondary_namespaces
Args : newvalue (optional)
=cut
sub secondary_namespaces {
my ( $obj, @values ) = @_;
if (@values) {
push( @{ $obj->{'secondary_namespaces'} }, @values );
}
return @{ $obj->{'secondary_namespaces'} || [] };
}
## These are indexing routines to index commonly used format - fasta
## swissprot and embl
sub new_SWISSPROT_index {
my ( $self, $index_dir, @files ) = @_;
my %secondary_patterns;
my $start_pattern = "^ID (\\S+)";
my $primary_pattern = "^AC (\\S+)\\;";
$secondary_patterns{"ID"} = $start_pattern;
my $index = Bio::DB::Flat::BinarySearch->new(
-index_dir => $index_dir,
-format => 'swissprot',
-primary_pattern => $primary_pattern,
-primary_namespace => "ACC",
-start_pattern => $start_pattern,
-secondary_patterns => \%secondary_patterns
);
$index->build_index(@files);
}
sub new_EMBL_index {
my ( $self, $index_dir, @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 = Bio::DB::Flat::BinarySearch->new(
-index_dir => $index_dir,
-format => 'embl',
-primary_pattern => $primary_pattern,
-primary_namespace => "ACC",
-start_pattern => $start_pattern,
-secondary_patterns => \%secondary_patterns
);
$index->build_index(@files);
return $index;
}
sub new_FASTA_index {
my ( $self, $index_dir, @files ) = @_;
my %secondary_patterns;
my $start_pattern = "^>";
my $primary_pattern = "^>(\\S+)";
my $primary_namespace = "ACC";
$secondary_patterns{"ID"} = "^>\\S+ +(\\S+)";
my $index = Bio::DB::Flat::BinarySearch->new(
-index_dir => $index_dir,
-format => 'fasta',
-primary_pattern => $primary_pattern,
-primary_namespace => "ACC",
-start_pattern => $start_pattern,
-secondary_patterns => \%secondary_patterns
);
$index->build_index(@files);
return $index;
}
# EVERYTHING THAT FOLLOWS THIS
# is an awful hack - in reality Michele's code needs to be rewritten
# to use Bio::SeqIO, but I have too little time to do this -- LS
sub guess_alphabet {
my $self = shift;
my $line = shift;
my $format = $self->format;
return 'protein' if $format eq 'swissprot';
if ( $format eq 'genbank' ) {
return unless $line =~ /^LOCUS/;
return 'dna' if $line =~ /\s+\d+\s+bp/i;
return 'protein';
}
if ( $format eq 'embl' ) {
return unless $line =~ /^ID/;
return 'dna' if $line =~ / DNA;/i;
return 'rna' if $line =~ / RNA;/i;
return 'protein';
}
return;
}
# return (namespace,primary_pattern,start_pattern,secondary_pattern)
sub _guess_patterns {
my $self = shift;
my $format = shift;
if ( $format =~ /swiss(prot)?/i ) {
return ( 'ID', "^ID (\\S+)", "^ID (\\S+)",
{ ACC => "^AC (\\S+);" } );
}
if ($format =~ /embl/i) {
return ('ID',
"^ID (\\S+[^; ])",
"^ID (\\S+[^; ])",
{
ACC => q/^AC (\S+);/,
VERSION => q/^SV\s+(\S+)/
});
}
if ( $format =~ /genbank/i ) {
return (
'ID',
q/^LOCUS\s+(\S+)/,
q/^LOCUS/,
{
ACC => q/^ACCESSION\s+(\S+)/,
VERSION => q/^VERSION\s+(\S+)/
}
);
}
if ( $format =~ /fasta/i ) {
return ( 'ACC', '^>(\S+)', '^>(\S+)', );
}
$self->throw("I can't handle format $format");
}
1;