Summary

Bio::SeqIO::embl - EMBL sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

It is probably best not to use this object directly, but
rather go through the AnnSeqIO handler system. Go:

    $stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL');

    while ( (my $seq = $stream->next_seq()) ) {
	# do something with $seq
    }

Description

This object can transform Bio::Seq objects to and from EMBL flat
file databases.
There is alot of flexibility here about how to dump things which I need
to document fully.
There should be a common object that this and genbank share (probably
with swissprot). Too much of the magic is identical.    (output only) shows the dna or not
   (output only) provides a sorting func which is applied to the FTHelpers
before printing
   This is function which is called as

   print "ID   ", $func($annseq), "\n";

   To generate the ID line. If it is not there, it generates a sensible ID
line using a number of tools.
   If you want to output annotations in embl format they need to be
stored in a Bio::Annotation::Collection object which is accessible
through the Bio::SeqI interface method annotation().
   The following are the names of the keys which are polled from a
Bio::Annotation::Collection object.
   reference - Should contain Bio::Annotation::Reference objects
comment - Should contain Bio::Annotation::Comment objects
dblink - Should contain Bio::Annotation::DBLink objects

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object (must be seq) to the stream
 Returns : 1 for success and 0 for error
 Args    : array of 1 to n Bio::SeqI objects

 Title   : _print_EMBL_FTHelper
 Usage   :
 Function: Internal function
 Returns : 
 Args    :

 Title   : _read_EMBL_References
 Usage   :
 Function: Reads references from EMBL format. Internal function really
 Example :
 Returns : 
 Args    :

 Title   : _read_EMBL_Species
 Usage   :
 Function: Reads the EMBL Organism species and classification
           lines.
 Example :
 Returns : A Bio::Species object
 Args    : a reference to the current line buffer

 Title   : _read_EMBL_DBLink
 Usage   :
 Function: Reads the EMBL database cross reference ("DR") lines
 Example :
 Returns : A list of Bio::Annotation::DBLink objects
 Args    :

 Title   : _filehandle
 Usage   : $obj->_filehandle($newval)
 Function: 
 Example : 
 Returns : value of _filehandle
 Args    : newvalue (optional)

 Title   : _read_FTHelper_EMBL
 Usage   : _read_FTHelper_EMBL($buffer)
 Function: reads the next FT key line
 Example :
 Returns : Bio::SeqIO::FTHelper object 
 Args    : filehandle and reference to a scalar

 Title   : _write_line_EMBL
 Usage   :
 Function: internal function
 Example :
 Returns : 
 Args    :

 Title   : _write_line_EMBL_regex
 Usage   :
 Function: internal function for writing lines of specified
           length, with different first and the next line 
           left hand headers and split at specific points in the
           text
 Example :
 Returns : nothing
 Args    : file handle, first header, second header, text-line, regex for line breaks, total line length

 Title   : _post_sort
 Usage   : $obj->_post_sort($newval)
 Function: 
 Returns : value of _post_sort
 Args    : newvalue (optional)

 Title   : _show_dna
 Usage   : $obj->_show_dna($newval)
 Function: 
 Returns : value of _show_dna
 Args    : newvalue (optional)

 Title   : _id_generation_func
 Usage   : $obj->_id_generation_func($newval)
 Function: 
 Returns : value of _id_generation_func
 Args    : newvalue (optional)

 Title   : _ac_generation_func
 Usage   : $obj->_ac_generation_func($newval)
 Function: 
 Returns : value of _ac_generation_func
 Args    : newvalue (optional)

 Title   : _sv_generation_func
 Usage   : $obj->_sv_generation_func($newval)
 Function: 
 Returns : value of _sv_generation_func
 Args    : newvalue (optional)

 Title   : _kw_generation_func
 Usage   : $obj->_kw_generation_func($newval)
 Function: 
 Returns : value of _kw_generation_func
 Args    : newvalue (optional)

Methods code

sub _initialize {

  my($self,@args) = @_;

  $self->SUPER::_initialize(@args);  
  # hash for functions for decoding keys.
  $self->{'_func_ftunit_hash'} = {}; 
  $self->_show_dna(1); # sets this to one by default. People can change it 
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory
			      (-verbose => $self->verbose(), 
			       -type => 'Bio::Seq::RichSeq'));
  }

}

sub next_seq {

   my ($self,@args) = @_;
   my ($pseq,$c,$line,$name,$desc,$acc,$seqc,$mol,$div, 
       $date, $comment, @date_arr);

   my ($annotation, %params, @features) = ( new Bio::Annotation::Collection);

   $line = $self->_readline;   # This needs to be before the first eof() test

   if( !defined $line ) {
       return undef; # no throws - end of file
   }

   if( $line =~ /^\s+$/ ) {
       while( defined ($line = $self->_readline) ) {
	   $line =~/^\S/ && last;
       }
   }   
   if( !defined $line ) {
       return undef; # end of file
   }
   $line =~ /^ID\s+\S+/ || $self->throw("EMBL stream with no ID. Not embl in my book");
   $line =~ /^ID\s+(\S+)\s+\S+\;\s+([^;]+)\;\s+(\S+)\;/;
   $name = $1;
   $mol = $2;
   $div = $3;
   if(! $name) {
       $name = "unknown id";
   }
   my $alphabet;

    # this is important to have the id for display in e.g. FTHelper, otherwise
    # you won't know which entry caused an error
   if($mol) {
       if ( $mol =~ /circular/ ) {
	   $params{'-is_circular'} = 1;
	   $mol =~  s|circular ||;
       }
       if (defined $mol ) {	   
	   if ($mol =~ /DNA/) {
	       $alphabet='dna';
	   }
	   elsif ($mol =~ /RNA/) {
	       $alphabet='rna';
	   }
	   elsif ($mol =~ /AA/) {
	       $alphabet='protein';
	   }
       }

   }
   
#   $self->warn("not parsing upper annotation in EMBL file yet!");
   my $buffer = $line;

   local $_;
 
   BEFORE_FEATURE_TABLE :
   until( !defined $buffer ) {
       $_ = $buffer;

       # Exit at start of Feature table
       last if /^F[HT]/;

       # Description line(s)
       if (/^DE\s+(\S.*\S)/) {
           $desc .= $desc ? " $1" : $1;
       }

       #accession number
       if( /^AC\s+(.*)?/ ) {
	   my @accs = split(/[; ]+/, $1); # allow space in addition
	   $params{'-accession_number'} = shift @accs 
	       unless defined $params{'-accession_number'};
	   push @{$params{'-secondary_accessions'}}, @accs;
       }
       
       #version number
       if( /^SV\s+\S+\.(\d+);?/ ) {
	   my $sv = $1;
	   #$sv =~ s/\;//;
	   $params{'-seq_version'} = $sv;
	   $params{'-version'} = $sv;
       }

       #date (NOTE: takes last date line)
       if( /^DT\s+(.+)$/ ) {
	   my $date = $1;
	   push @{$params{'-dates'}},$date;
       }
       
       #keywords
       if( /^KW   (.*)\S*$/ ) {
	   my @kw = split(/\s*\;\s*/,$1);
	   
	   push @{$params{'-keywords'}}, @kw;
       }

       # Organism name and phylogenetic information
       elsif (/^O[SC]/) {
           my $species = $self->_read_EMBL_Species(\$buffer);
           $params{'-species'}= $species;
       }

       # References
       elsif (/^R/) {
	   my @refs = $self->_read_EMBL_References(\$buffer);
	   foreach my $ref ( @refs ) {
	       $annotation->add_Annotation('reference',$ref);
	   }
       }
       
       # DB Xrefs
       elsif (/^DR/) {
	   my @links = $self->_read_EMBL_DBLink(\$buffer);
	   foreach my $dblink ( @links ) {
	       $annotation->add_Annotation('dblink',$dblink);
	   }
       }
       
       # Comments
       elsif (/^CC\s+(.*)/) {
	   $comment .= $1;
	   $comment .= " ";
	   while (defined ($_ = $self->_readline) ) {
	       if (/^CC\s+(.*)/) {
		   $comment .= $1;
		   $comment .= " ";
	       }
	       else { 
		   last;
	       }
	   }
	   my $commobj = Bio::Annotation::Comment->new();
	   $commobj->text($comment);
	   $annotation->add_Annotation('comment',$commobj);
	   $comment = "";
       }

       # Get next line.
       $buffer = $self->_readline;
   }

   while( defined ($_ = $self->_readline) ) {
       /^FT   \w/ && last;
       /^SQ / && last;
       /^CO / && last;
   }
   $buffer = $_;

   if (defined($buffer) && $buffer =~ /^FT /) {
     until( !defined ($buffer) ) {
	 my $ftunit = $self->_read_FTHelper_EMBL(\$buffer);
	 # process ftunit

	 push(@features,
	      $ftunit->_generic_seqfeature($self->location_factory(), $name));

	 if( $buffer !~ /^FT/ ) {
	     last;
	 }
     }
   }


   # skip comments
   while( defined ($buffer) && $buffer =~ /^XX/ ) { 
       $buffer = $self->_readline();
   }
   
   if( $buffer =~ /^CO/  ) {	   
       until( !defined ($buffer) ) {
	   my $ftunit = $self->_read_FTHelper_EMBL(\$buffer);
	   # process ftunit
	   push(@features,
		$ftunit->_generic_seqfeature($self->location_factory(),
					     $name));
	   
	   if( $buffer !~ /^CO/ ) {
	       last;
	   }
       }       
   }
   if( $buffer !~ /^SQ/  ) {
       while( defined ($_ = $self->_readline) ) {
	   /^SQ/ && last;
       }
   }
   
   $seqc = "";	       
   while( defined ($_ = $self->_readline) ) {
       /^\/\// && last;
       $_ = uc($_);
       s/[^A-Za-z]//g;
       $seqc .= $_;
   }
   my $seq = $self->sequence_factory->create
       (-verbose => $self->verbose(),
	-division => $div,
	-seq => $seqc,
	-desc => $desc,
	-display_id => $name,
	-annotation => $annotation,
	-molecule => $mol,
	-alphabet => $alphabet,
	-features =>\@ features,
	%params);

   return $seq;

}

sub write_seq {

    my ($self,@seqs) = @_;

    foreach my $seq ( @seqs ) { 
	$self->throw("Attempting to write with no seq!") unless defined $seq;
	unless ( ref $seq && $seq->isa('Bio::SeqI' ) ) {
	    $self->warn("$seq is not a SeqI compliant sequence object!") 
		if $self->verbose >= 0;
	    unless ( ref $seq && $seq->isa('Bio::PrimarySeqI' ) ) {
		$self->throw("$seq is not a PrimarySeqI compliant sequence object!");
	    }
	}
	my $str = $seq->seq || '';

	my $mol;
	my $div;
	my $len = $seq->length();

	if ($seq->can('division') && defined $seq->division) {
	    $div = $seq->division();
	}
	$div ||= 'UNK';

	if ($seq->can('molecule')) {
	    $mol = $seq->molecule();
	    $mol = 'RNA' if defined $mol && $mol =~ /RNA/; # no 'mRNA' 
	}
	elsif ($seq->can('primary_seq') && defined $seq->primary_seq->alphabet) {
	    my $alphabet =$seq->primary_seq->alphabet;
	    if ($alphabet eq 'dna') {
		$mol ='DNA';
	    }
	    elsif ($alphabet eq 'rna') {
		$mol='RNA';
	    }
	    elsif ($alphabet eq 'protein') {
		$mol='AA';
	    }
	}
	$mol ||= 'XXX';
	$mol = "circular $mol" if $seq->is_circular;

	my $temp_line;
	if( $self->_id_generation_func ) {
	    $temp_line = &{$self->_id_generation_func}($seq);
	} else {

            $self->warn("No whitespace allowed in EMBL display id [". $seq->display_id. "]")
                if $seq->display_id =~ /\s/;

	    $temp_line = sprintf("%-11sstandard; $mol; $div; %d BP.", $seq->id(), $len);
	} 

	$self->_print( "ID   $temp_line\n","XX\n");

	# Write the accession line if present
	my( $acc );
	{
	    if( my $func = $self->_ac_generation_func ) {
		$acc = &{$func}($seq);
	    } elsif( $seq->isa('Bio::Seq::RichSeqI') && 
		     defined($seq->accession_number) ) {
		$acc = $seq->accession_number;
		$acc = join("; ", $acc, $seq->get_secondary_accessions);
	    } elsif ( $seq->can('accession_number') ) {
		$acc = $seq->accession_number;
	    }

	    if (defined $acc) {
		$self->_print("AC   $acc;\n",
			      "XX\n");
	    }
	}

	# Write the sv line if present
	{
	    my( $sv );
	    if (my $func = $self->_sv_generation_func) {
		$sv = &{$func}($seq);
	    } elsif($seq->isa('Bio::Seq::RichSeqI') && 
		    defined($seq->seq_version)) {
                my ($prim_acc) = $acc =~ /([^;]+)/;
		$sv = "$prim_acc.". $seq->seq_version();
	    }	
	    if (defined $sv) {
		$self->_print( "SV   $sv\n",
			       "XX\n");
	    }
	}

	# Date lines
	my $switch=0;
	if( $seq->can('get_dates') ) {
	    foreach my $dt ( $seq->get_dates() ) {
		$self->_write_line_EMBL_regex("DT   ","DT   ",$dt,'\s+|$',80);#'
		    $switch=1;
	    }
	    if ($switch == 1) {
		$self->_print("XX\n");
	    }
	}

	# Description lines
	$self->_write_line_EMBL_regex("DE   ","DE   ",$seq->desc(),'\s+|$',80);	#'
	$self->_print( "XX\n");

	# if there, write the kw line
	{
	    my( $kw );
	    if( my $func = $self->_kw_generation_func ) {
		$kw = &{$func}($seq);
	    } elsif( $seq->can('keywords') ) {
		$kw = $seq->keywords;
	    }
	    if (defined $kw) {
		$self->_write_line_EMBL_regex("KW   ", "KW   ", $kw, '\s+|$', 80); #'
		$self->_print( "XX\n");
	    }
	}

	# Organism lines

	if ($seq->can('species') && (my $spec = $seq->species)) {
	    my($species, @class) = $spec->classification();
	    my $genus = $class[0];
	    my $OS = "$genus $species";
	    if (my $ssp = $spec->sub_species) {
		$OS .= " $ssp";
	    }
	    if (my $common = $spec->common_name) {
		$OS .= " ($common)";
	    }
	    $self->_print("OS   $OS\n");
	    my $OC = join('; ', reverse(@class)) .'.';
	    $self->_write_line_EMBL_regex("OC   ","OC   ",$OC,'; |$',80); #'
	    if ($spec->organelle) {
		$self->_write_line_EMBL_regex("OG   ","OG   ",$spec->organelle,'; |$',80); #'
	    }
	    $self->_print("XX\n");
	}

	# Reference lines
	my $t = 1;
	if ( $seq->can('annotation') && defined $seq->annotation ) {
	    foreach my $ref ( $seq->annotation->get_Annotations('reference') ) {
		$self->_print( "RN   [$t]\n");

		# Having no RP line is legal, but we need both
		# start and end for a valid location.
		my $start = $ref->start;
		my $end   = $ref->end;
		if ($start and $end) {
		    $self->_print( "RP   $start-$end\n");
		} elsif ($start or $end) {
		    $self->throw("Both start and end are needed for a valid RP line.  Got: start='$start' end='$end'");
		}

		if (my $med = $ref->medline) {
		    $self->_print( "RX   MEDLINE; $med.\n");
		}
		if (my $pm = $ref->pubmed) {
		    $self->_print( "RX   PUBMED; $pm.\n");
		}
		$self->_write_line_EMBL_regex("RA   ", "RA   ", 
					      $ref->authors . ";",
					      '\s+|$', 80); #'

		# If there is no title to the reference, it appears
		# as a single semi-colon.  All titles must end in
		# a semi-colon.
		my $ref_title = $ref->title || '';
		$ref_title =~ s/[\s;]*$/;/;
		$self->_write_line_EMBL_regex("RT   ", "RT   ", $ref_title,    '\s+|$', 80); #'
		$self->_write_line_EMBL_regex("RL   ", "RL   ", $ref->location, '\s+|$', 80); #'
		if ($ref->comment) {
		    $self->_write_line_EMBL_regex("RC   ", "RC   ", $ref->comment, '\s+|$', 80); #' 
		}
		$self->_print("XX\n");
		$t++;
	    }


	    # DB Xref lines
	    if (my @db_xref = $seq->annotation->get_Annotations('dblink') ) {
		foreach my $dr (@db_xref) {
		    my $db_name = $dr->database;
		    my $prim    = $dr->primary_id;
		    my $opt     = $dr->optional_id || '';

		    my $line = "$db_name; $prim; $opt.";
		    $self->_write_line_EMBL_regex("DR   ", "DR   ", $line, '\s+|$', 80); #'
		}
		$self->_print("XX\n");
	    }

	    # Comment lines
	    foreach my $comment ( $seq->annotation->get_Annotations('comment') ) {
		$self->_write_line_EMBL_regex("CC   ", "CC   ", $comment->text, '\s+|$', 80); #'
		$self->_print("XX\n");
	    }
	}
	# "\\s\+\|\$"

	## FEATURE TABLE

	$self->_print("FH   Key             Location/Qualifiers\n");
	$self->_print("FH\n");

	my @feats = $seq->can('top_SeqFeatures') ? $seq->top_SeqFeatures : ();
	if ($feats[0]) {
	    if( defined $self->_post_sort ) {
		# we need to read things into an array. 
		# Process. Sort them. Print 'em

		my $post_sort_func = $self->_post_sort();
		my @fth;

		foreach my $sf ( @feats ) {
		    push(@fth,Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq));
		}

		@fth = sort { &$post_sort_func($a,$b) } @fth;

		foreach my $fth ( @fth ) {
		    $self->_print_EMBL_FTHelper($fth);
		}
	    } else {
		# not post sorted. And so we can print as we get them.
		# lower memory load...

		foreach my $sf ( @feats ) {
		    my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq);
		    foreach my $fth ( @fth ) {
			if( $fth->key eq 'CONTIG') {
			    $self->_show_dna(0);
			}
			$self->_print_EMBL_FTHelper($fth);
		    }
		}
	    }
	}

	if( $self->_show_dna() == 0 ) {
	    $self->_print( "//\n");
	    return;
	}
	$self->_print( "XX\n");

	# finished printing features.
	
	$str =~ tr/A-Z/a-z/;

	# Count each nucleotide
	my $alen = $str =~ tr/a/a/;
	my $clen = $str =~ tr/c/c/;
	my $glen = $str =~ tr/g/g/;
	my $tlen = $str =~ tr/t/t/;

	my $olen = $len - ($alen + $tlen + $clen + $glen);
	if( $olen < 0 ) {
	    $self->warn("Weird. More atgc than bases. Problem!");
	}

	$self->_print("SQ   Sequence $len BP; $alen A; $clen C; $glen G; $tlen T; $olen other;\n");

	my $nuc = 60;		# Number of nucleotides per line
	my $whole_pat = 'a10' x 6; # Pattern for unpacking a whole line
	my $out_pat   = 'A11' x 6; # Pattern for packing a line
	my $length = length($str);

	# Calculate the number of nucleotides which fit on whole lines
	my $whole = int($length / $nuc) * $nuc;

	# Print the whole lines
	my( $i );
	for ($i = 0; $i < $whole; $i += $nuc) {
	    my $blocks = pack $out_pat,
	    unpack $whole_pat,
	    substr($str, $i, $nuc);
	    $self->_print(sprintf("     $blocks%9d\n", $i + $nuc));
	}

	# Print the last line
	if (my $last = substr($str, $i)) {
	    my $last_len = length($last);
	    my $last_pat = 'a10' x int($last_len / 10) .'a'. $last_len % 10;
	    my $blocks = pack $out_pat,
	    unpack($last_pat, $last);
	    $self->_print(sprintf("     $blocks%9d\n", $length)); # Add the length to the end
	}

	$self->_print( "//\n");

	$self->flush if $self->_flush_on_write && defined $self->_fh;
	return 1;
    }

}

sub _print_EMBL_FTHelper {

   my ($self,$fth) = @_;
   
   if( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) {
       $fth->warn("$fth is not a FTHelper class. Attempting to print, but there could be tears!");
   }
   

   #$self->_print( "FH   Key             Location/Qualifiers\n");
   #$self->_print( sprintf("FT   %-15s  %s\n",$fth->key,$fth->loc));
   # let
   if( $fth->key eq 'CONTIG' ) {
       $self->_print("XX\n");
       $self->_write_line_EMBL_regex("CO   ",
				     "CO   ",$fth->loc,
				     '\,|$',80); #'
       return;
   } 
   $self->_write_line_EMBL_regex(sprintf("FT   %-15s ",$fth->key),
				 "FT                   ",$fth->loc,
				 '\,|$',80); #'
   foreach my $tag ( keys %{$fth->field} ) {
       if( ! defined $fth->field->{$tag} ) { next; } 
       foreach my $value ( @{$fth->field->{$tag}} ) {
	   $value =~ s/\"/\"\"/g;
	   if ($value eq "_no_value") {
	       $self->_write_line_EMBL_regex("FT                   ",
					     "FT                   ",
					     "/$tag",'.|$',80); #'
	   }
           # there are almost 3x more quoted qualifier values and they
           # are more common too so we take quoted ones first
           elsif (!$FTQUAL_NO_QUOTE{$tag}) {
              my $pat = $value =~ /\s/ ? '\s|\-|$' : '.|\-|$';
	      $self->_write_line_EMBL_regex("FT                   ",
					    "FT                   ",
					    "/$tag=\"$value\"",$pat,80);
           } else {
              $self->_write_line_EMBL_regex("FT                   ",
					    "FT                   ",
					    "/$tag=$value",'.|$',80); #'
           }
       }
   }

}

sub _read_EMBL_References {

   my ($self,$buffer) = @_;
   my (@refs);
   
   # assumme things are starting with RN

   if( $$buffer !~ /^RN/ ) {
       warn("Not parsing line '$$buffer' which maybe important");
   }
   my $b1;
   my $b2;
   my $title;
   my $loc;
   my $au;
   my $med;
   my $pm;
   my $com;

   while( defined ($_ = $self->_readline) ) {
       /^R/ || last;
       /^RP   (\d+)-(\d+)/ && do {$b1=$1;$b2=$2;};
       /^RX   MEDLINE;\s+(\d+)/ && do {$med=$1};
       /^RX   PUBMED;\s+(\d+)/ && do {$pm=$1};       
       /^RA   (.*)/ && do {
	   $au = $self->_concatenate_lines($au,$1); next;
       };
       /^RT   (.*)/ && do {
	   $title = $self->_concatenate_lines($title,$1); next;
       };
       /^RL   (.*)/ && do {
	   $loc = $self->_concatenate_lines($loc,$1); next;
       };
       /^RC   (.*)/ && do {
	   $com = $self->_concatenate_lines($com,$1); next;
       };
   }
   
   my $ref = new Bio::Annotation::Reference;
   $au =~ s/;\s*$//g;
   $title =~ s/;\s*$//g;

   $ref->start($b1);
   $ref->end($b2);
   $ref->authors($au);
   $ref->title($title);
   $ref->location($loc);
   $ref->medline($med);
   $ref->comment($com);
   $ref->pubmed($pm);

   push(@refs,$ref);
   $$buffer = $_;
   
   return @refs;

}

sub _read_EMBL_Species {

    my( $self, $buffer ) = @_;
    my $org;

    $_ = $$buffer;
    my( $sub_species, $species, $genus, $common, @class, $ns_name );
    while (defined( $_ ||= $self->_readline )) {

        if (/^OS\s+((\S+)(?:\s+([^\(]\S*))?(?:\s+([^\(]\S*))?(?:\s+\((.*)\))?)/) {
            $ns_name = $1;
            $genus   = $2;
	    $species = $3 || 'sp.';
	    $sub_species = $4 if $4;
            $common      = $5 if $5;
        }
        elsif (s/^OC\s+//) {
	    # only split on ';' or '.' so that 
	    # classification that is 2 words will 
	    # still get matched
	    # use map to remove trailing/leading spaces
	    chomp;
            push(@class,  map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/);
        }
	elsif (/^OG\s+(.*)/) {
	    $org = $1;
	}
        else {
            last;
        }

        $_ = undef; # Empty $_ to trigger read of next line
    }

    $$buffer = $_;

    # Don't make a species object if it is "Unknown" or "None"
    return if $genus =~ /^(Unknown|None)$/i;

    # Bio::Species array needs array in Species -> Kingdom direction
    if ($class[0] eq 'Viruses') {
        push( @class, $ns_name );
    }
    elsif ($class[$#class] eq $genus) {
        push( @class, $species );
    } else {
        push( @class, $genus, $species );
    }
    @class = reverse @class;

    my $make = Bio::Species->new();
    $make->classification(\@ class, "FORCE" );  # no name validation please
    $make->common_name( $common      ) if $common;
    unless ($class[-1] eq 'Viruses') {
        $make->sub_species( $sub_species ) if $sub_species;
    }
    $make->organelle  ( $org         ) if $org;
    return $make;

}

sub _read_EMBL_DBLink {

    my( $self,$buffer ) = @_;
    my( @db_link );

    $_ = $$buffer;
    while (defined( $_ ||= $self->_readline )) {
        
        if (my($databse, $prim_id, $sec_id)
                = /^DR   ([^\s;]+);\s*([^\s;]+);\s*([^\s;]+)?\.$/) {
            my $link = Bio::Annotation::DBLink->new();
            $link->database   ( $databse );
            $link->primary_id ( $prim_id );
            $link->optional_id( $sec_id  ) if $sec_id;
            push(@db_link, $link);
	}
        else {
            last;
        }
        
        $_ = undef; # Empty $_ to trigger read of next line
    }
    
    $$buffer = $_;
    
    return @db_link;

}

sub _filehandle {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_filehandle'} = $value;
    }
    return $obj->{'_filehandle'};

}

sub _read_FTHelper_EMBL {

    my ($self,$buffer) = @_;
    
    my ($key,   # The key of the feature
        $loc,   # The location line from the feature
        @qual,  # An arrray of lines making up the qualifiers
	);
    
    if ($$buffer =~ /^FT\s{3}(\S+)\s+(\S+)/) {
        $key = $1;
        $loc = $2;
        # Read all the lines up to the next feature
        while ( defined($_ = $self->_readline) ) {
            if (/^FT(\s+)(.+?)\s*$/) {
                # Lines inside features are preceeded by 19 spaces
                # A new feature is preceeded by 3 spaces
                if (length($1) > 4) {
                    # Add to qualifiers if we're in the qualifiers
                    if (@qual) {
                        push(@qual, $2);
                    }
                    # Start the qualifier list if it's the first qualifier
                    elsif (substr($2, 0, 1) eq '/') {
                        @qual = ($2);
                    }
                    # We're still in the location line, so append to location
                    else {
                        $loc .= $2;
                    }
                } else {
                    # We've reached the start of the next feature
                    last;
                }
            } else {
                # We're at the end of the feature table
                last;
            }
        }
    } elsif( $$buffer =~ /^CO\s+(\S+)/) {
	$key = 'CONTIG';
	$loc = $1;
	# Read all the lines up to the next feature
	while ( defined($_ = $self->_readline) ) {
	    if (/^CO\s+(\S+)\s*$/) {
		$loc .= $1;
	    } else {
		# We've reached the start of the next feature
		last;
	    }
	}
    } else {
        # No feature key
        return;
    }
    
    # Put the first line of the next feature into the buffer
    $$buffer = $_;

    # Make the new FTHelper object
    my $out = new Bio::SeqIO::FTHelper();
    $out->verbose($self->verbose());
    $out->key($key);
    $out->loc($loc);

    # Now parse and add any qualifiers.  (@qual is kept
    # intact to provide informative error messages.)
  QUAL: for (my $i = 0; $i < @qual; $i++) {
        $_ = $qual[$i];
        my( $qualifier, $value ) = m{^/([^=]+)(?:=(.+))?}
            or $self->throw("Can't see new qualifier in: $_\nfrom:\n"
                . join('', map "$_\n", @qual));
        if (defined $value) {
            # Do we have a quoted value?
            if (substr($value, 0, 1) eq '"') {
                # Keep adding to value until we find the trailing quote
                # and the quotes are balanced
                while ($value !~ /"$/ or $value =~ tr/"/"/ % 2) { #"
                    $i++;
                    my $next = $qual[$i];
                    unless (defined($next)) {
                        warn("Unbalanced quote in:\n", map("$_\n", @qual),
                            "No further qualifiers will be added for this feature");
                        last QUAL;
                    }

                    # Join to value with space if value or next line contains a space
                    $value .= (grep /\s/, ($value, $next)) ? " $next" : $next;
                }
                # Trim leading and trailing quotes
                $value =~ s/^"|"$//g;
                # Undouble internal quotes
                $value =~ s/""/"/g; #"
            }
        } else {
            $value = '_no_value';
        }

        # Store the qualifier
        $out->field->{$qualifier} ||= [];
        push(@{$out->field->{$qualifier}},$value);
    }   

    return $out;

}

sub _write_line_EMBL {

   my ($self,$pre1,$pre2,$line,$length) = @_;

   $length || die "Miscalled write_line_EMBL without length. Programming error!";
   my $subl = $length - length $pre2;
   my $linel = length $line;
   my $i;

   my $sub = substr($line,0,$length - length $pre1);

   $self->_print( "$pre1$sub\n");
   
   for($i= ($length - length $pre1);$i < $linel;) {
       $sub = substr($line,$i,($subl));
       $self->_print( "$pre2$sub\n");
       $i += $subl;
   }

}

sub _write_line_EMBL_regex {

    my ($self,$pre1,$pre2,$line,$regex,$length) = @_;

    #print STDOUT "Going to print with $line!\n";

    $length || die "Programming error - called write_line_EMBL_regex without length.";

#    if( length $pre1 != length $pre2 ) {
#      $self->throw(<<END);
#Programming error - called write_line_EMBL_regex with different length pre1 and pre2 tags!
#pre1 = $pre1
#pre2 = $pre2
#END
#    }

    my $subl = $length - (length $pre1) -1 ;



    my( @lines );
    while(defined $line && 
	  $line =~ m/(.{1,$subl})($regex)/g) {
	push(@lines, $1.$2);
    }
    foreach (@lines) { s/\s+$//; }
    
    # Print first line
    my $s = shift(@lines) || '';    
    $self->_print( "$pre1$s\n");
    
    # Print the rest
    foreach my $s ( @lines ) {
	$s = '' if( !defined $s );
        $self->_print( "$pre2$s\n");
    }

}

sub _post_sort {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_post_sort'} = $value;
    }
    return $obj->{'_post_sort'};

}

sub _show_dna {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_show_dna'} = $value;
    }
    return $obj->{'_show_dna'};

}

sub _id_generation_func {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_id_generation_func'} = $value;
    }
    return $obj->{'_id_generation_func'};

}

sub _ac_generation_func {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_ac_generation_func'} = $value;
    }
    return $obj->{'_ac_generation_func'};

}

sub _sv_generation_func {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_sv_generation_func'} = $value;
    }
    return $obj->{'_sv_generation_func'};

}

sub _kw_generation_func {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_kw_generation_func'} = $value;
    }
    return $obj->{'_kw_generation_func'};

}

General documentation

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
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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/

Email birney@ebi.ac.uk
Describe contact details here

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _