Public Member Functions
public Bio::EnsEMBL::Utils::SeqDumper	new ()

public void	enable_feature_type ()

public void	attach_database ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	get_database ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	remove_database ()

public void	disable_feature_type ()

public void	is_enabled ()

public void	dump ()

public void	dump_embl ()

public void	dump_genbank ()

protected void	_dump_feature_table ()

public	transcript_to_codon_start ()

protected Int	_get_codon_table_id ()

public void	dump_fasta ()

public String	features2location ()

public String	annotation_source ()

protected	_date_string ()

public	write ()

public	write_genbank_seq ()

public	write_genbank_seq ()

public	write_embl_seq ()

public	print ()

Detailed Description

Synopsis

$seq_dumper = Bio::EnsEMBL::Utils::SeqDumper->new();
 
# don't dump snps or repeats
$seq_dumper->disable_feature_type('repeat');
$seq_dumper->disable_feature_type('variation');
 
# dump EMBL format to STDOUT
$seq_dumper->dump( $slice, 'EMBL' );
 
# dump GENBANK format to a file
$seq_dumper->dump( $slice, 'GENBANK', 'out.genbank' );
 
# dump FASTA format to a file
$seq_dumper->dump( $slice, 'FASTA', 'out.fasta' );

Description

A relatively simple and lite-weight flat file dumper for Ensembl slices.
The memory efficiency could be improved and this is currently not very
good for dumping very large sequences such as whole chromosomes.

Definition at line 33 of file SeqDumper.pm.

Member Function Documentation

◆ _date_string()

protected Bio::EnsEMBL::Utils::SeqDumper::_date_string ( )

Undocumented method

Code:

click to view

◆ _dump_feature_table()

protected void Bio::EnsEMBL::Utils::SeqDumper::_dump_feature_table ( )

  Arg [1]    : Bio::EnsEMBL::Slice slice
  Example    :

none

  Description: Helper method used to dump feature tables used in EMBL, FASTA,
               GENBANK.  Assumes formating of file handle has been setup
               already to use $FEAT and $VALUE values.
  Returntype : none
  Exceptions : none
  Caller     : internal

Code:

click to view

sub _dump_feature_table {
  my $self   = shift;
  my $slice  = shift;
  my $FH     = shift;
  my $FORMAT = shift;
 
  #use only the core database to dump features (except for bloody snps)
  my $lite = $slice->adaptor->db->remove_db_adaptor('lite');
 
  my $meta = $slice->adaptor->db->get_MetaContainer;
 
  #lump file handle and format string together for simpler method calls
  my @ff = ($FH, $FORMAT);
  my $value;
 
  #source
  my $classification = join(', ', @{$meta->get_classification()});
  $self->write(@ff,'source', "1.." . $slice->length());
  $self->write(@ff,''      , '/organism="'.$meta->get_scientific_name(). '"');
  $self->write(@ff,''      , '/db_xref="taxon:'.$meta->get_taxonomy_id().'"');
 
  #
  # Transcripts & Genes
  #
  my @gene_slices;
  if($self->is_enabled('gene')) {
    push @gene_slices, $slice;
  }
 
  # Retrieve slices of other database where we need to pull genes from
 
  my $gene_dbs = {'vegagene' => 'vega',
                  'estgene'  => 'estgene'};
 
  foreach my $gene_type (keys %$gene_dbs) {
    if($self->is_enabled($gene_type)) {
      my $db = $self->get_database($gene_dbs->{$gene_type});
      if($db) {
        my $sa = $db->get_SliceAdaptor();
        push @gene_slices, $sa->fetch_by_name($slice->name());
      } else {
        warning("A [". $gene_dbs->{$gene_type} ."] database must be " .
                "attached to this SeqDumper\n(via a call to " .
                "attach_database) to retrieve genes of type [$gene_type]");
      }
    }
  }
 
  foreach my $gene_slice (@gene_slices) {
    my @genes = @{$gene_slice->get_all_Genes(undef,undef, 1)};
    while(my $gene = shift @genes) {
      $value = $self->features2location( [$gene] );
      $self->write( @ff, 'gene', $value );
      $self->write( @ff, "", '/gene='.$gene->stable_id_version() );
 
 
      if(defined($gene->display_xref)){
    $self->write( @ff, "",'/locus_tag="'.$gene->display_xref->display_id.'"');
      }
      my $desc = $gene->description;
      if(defined($desc) and $desc ne ""){
    $desc =~ s/\"//; 
    $self->write( @ff, "", '/note="'.$gene->description.'"');
      }
 
 
 
      foreach my $transcript (@{$gene->get_all_Transcripts}) {
        my $translation = $transcript->translation;
 
        # normal transcripts get dumped differently than pseudogenes
        if($translation) {
          #normal transcript
          $value = $self->features2location($transcript->get_all_Exons);
          $self->write(@ff, 'mRNA', $value);
          $self->write(@ff,''   , '/gene="'.$gene->stable_id_version().'"');
          $self->write(@ff,''
                       ,'/standard_name="'.$transcript->stable_id_version().'"');
 
          # ...and a CDS section
          $value = 
            $self->features2location($transcript->get_all_translateable_Exons);
          $self->write(@ff,'CDS', $value);
          my $codon_start = $self->transcript_to_codon_start($transcript);
          $self->write(@ff,''   , qq{/codon_start="${codon_start}"}) if $codon_start > 1;
 
          my $codon_table_id = $self->_get_codon_table_id($slice);
          if($codon_table_id > 1){
            $self->write(@ff,''   , '/transl_table='.$codon_table_id);
          }
          $self->write(@ff,''   , '/gene="'.$gene->stable_id_version().'"'); 
          $self->write(@ff,''   , '/protein_id="'.$translation->stable_id_version().'"');
          $self->write(@ff,''   ,'/note="transcript_id='.$transcript->stable_id_version().'"');
 
          foreach my $dbl (@{$transcript->get_all_DBLinks}) {
            my $db_xref    = '/db_xref="'.$dbl->dbname().':'.$dbl->primary_id().'"';
            my $go_db_xref = '/db_xref="'.$dbl->primary_id().'"';
            $value  = ($dbl->dbname()=~/GO/) ? $go_db_xref : $db_xref; 
            $self->write(@ff, '', $value);
          }
 
      my $pep = $transcript->translate();
          if ($pep) {
        $value = '/translation="'.$pep->seq().'"';
        $self->write(@ff, '', $value);
      }
        } else {
          #pseudogene
          $value = $self->features2location($transcript->get_all_Exons);
          $self->write(@ff, 'misc_RNA', $value);
          $self->write(@ff,''   , '/gene="'.$gene->stable_id_version().'"');
          foreach my $dbl (@{$transcript->get_all_DBLinks}) {
            $value = '/db_xref="'.$dbl->dbname().':'.$dbl->primary_id().'"';
            $self->write(@ff, '', $value);
          }
          $self->write(@ff,''   , '/note="'.$transcript->biotype().'"');
          $self->write(@ff,''
                       ,'/standard_name="'.$transcript->stable_id_version().'"');
        }
      }
    }
 
    # exons
    foreach my $gene (@{$gene_slice->get_all_Genes(undef,undef,1)}) {
      foreach my $exon (@{$gene->get_all_Exons}) {
        $self->write(@ff,'exon', $self->features2location([$exon]));
        $self->write(@ff,''    , '/note="exon_id='.$exon->stable_id_version().'"');
      }
    }
  }
 
  #
  # genscans
  #
  if($self->is_enabled('genscan')) {
    my @genscan_exons;
    my @transcripts = @{$slice->get_all_PredictionTranscripts(undef,1)};
    while(my $transcript = shift @transcripts) {
      my $exons = $transcript->get_all_Exons();
      push @genscan_exons, @$exons;
      $self->write(@ff, 'mRNA', $self->features2location($exons));
      $self->write(@ff, '', '/product="'.$transcript->translate()->seq().'"');
      $self->write(@ff, '', '/note="identifier='.$transcript->stable_id_version.'"');
      $self->write(@ff, '', '/note="Derived by automated computational' .
           ' analysis using gene prediction method:' .
           $transcript->analysis->logic_name . '"');
    }
  }
 
  #
  # snps
  #
  if($self->is_enabled('variation') && $slice->can('get_all_VariationFeatures')) {
#    $slice->adaptor->db->add_db_adaptor('lite', $lite) if $lite;
 
    my @variations = @{$slice->get_all_VariationFeatures()};
    while(my $snp = shift @variations) {
      my $ss = $snp->start;
      my $se = $snp->end;
      #skip snps that hang off edge of slice
      next if($ss < 1 || $se > $slice->length); 
 
      $self->write(@ff, 'variation', "$ss..$se");
      $self->write(@ff, ''         , '/replace="'.$snp->allele_string.'"'); 
      #$self->write(@ff, ''         , '/evidence="'.$snp->status.'"'); 
      my $rs_id = $snp->variation_name();
      my $db = $snp->source_name();
#      foreach my $link ($snp->each_DBLink) {
#        my $id = $link->primary_id;
#        my $db = $link->database;
        $self->write(@ff, '', "/db_xref=\"$db:$rs_id\""); 
#      }
    }
 
#    $slice->adaptor->db->remove_db_adaptor('lite') if $lite;
  }
 
  #
  # similarity features
  #
  if($self->is_enabled('similarity')) {
    foreach my $sim (@{$slice->get_all_SimilarityFeatures}) {
      $self->write(@ff, 'misc_feature', $self->features2location([$sim]));
      $self->write(@ff, ''       , '/note="match: '.$sim->hseqname.
          ' : '.$sim->hstart.'..'.$sim->hend.'('.$sim->hstrand.')"');
    }
  }
 
  #
  # repeats
  #
  if($self->is_enabled('repeat')) {
    my @rfs = @{$slice->get_all_RepeatFeatures()};
 
    while(my $repeat = shift @rfs) {
      $self->write(@ff, 'repeat_region', $self->features2location([$repeat]));
      $self->write(@ff, ''    , '/note="' . $repeat->repeat_consensus->name.
           ' repeat: matches ' . $repeat->hstart.'..'.$repeat->hend .
           '('.$repeat->hstrand.') of consensus"');
    }
 
  }
 
  #
  # markers
  #
  if($self->is_enabled('marker') && $slice->can('get_all_MarkerFeatures')) {
    my @markers = @{$slice->get_all_MarkerFeatures()};
    while(my $mf = shift @markers) {
      $self->write(@ff, 'STS', $self->features2location([$mf]));
      if($mf->marker->display_MarkerSynonym) {
        $self->write(@ff, ''   , '/standard_name="' .
                     $mf->marker->display_MarkerSynonym->name . '"');
      }
 
 
      #grep out synonyms without a source
      my @synonyms = @{$mf->marker->get_all_MarkerSynonyms};
      @synonyms = grep {$_->source } @synonyms;
      foreach my $synonym (@synonyms) {
        $self->write(@ff, '', '/db_xref="'.$synonym->source.
                     ':'.$synonym->name.'"');
      }
      $self->write(@ff, '', '/note="map_weight='.$mf->map_weight.'"');
    }
  }
 
  #
  # contigs
  #
  if($self->is_enabled('contig')) {
    foreach my $segment (@{$slice->project('seqlevel')}) {
      my ($start, $end, $slice) = @$segment;
      $self->write(@ff, 'misc_feature',
                   $start .'..'. $end);
      $self->write(@ff, '', '/note="contig '.$slice->seq_region_name .
           ' ' . $slice->start . '..' . $slice->end .
            '(' . $slice->strand . ')"');
    }
  }
 
  $slice->adaptor->db->add_db_adaptor('lite', $lite) if $lite;
 
}

◆ _get_codon_table_id()

protected Int Bio::EnsEMBL::Utils::SeqDumper::_get_codon_table_id ( )

  Arg [1]    : Bio::EnsEMBL::Slice slice
  Example    :

none

  Description: Helper method to get codon_table seq region attribute
               codon_table defines the genetic code table used if other than the universal genetic code table (1)
               By default it is 1 and is not shown in flat files.
               If it is not equal to 1, then it is shown as a transl_table qualifier on the CDS feature.
  Returntype : int
  Caller     : internal

Code:

click to view

◆ annotation_source()

public String Bio::EnsEMBL::Utils::SeqDumper::annotation_source ( )

  Arg [1]    : Bio::EnsEMBL::DBSQL::MetaContainer
  Example    :

$seq_dumper->annotation_source($meta_container);

  Description: Constructs a string with gene annotation sources
  Returntype : string
  Exceptions : none
  Caller     : dump_embl, dump_genbank

Code:

click to view

◆ attach_database()

public void Bio::EnsEMBL::Utils::SeqDumper::attach_database ( )

  Arg [1]    : string name
  Arg [2]    : Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    :

$seq_dumper->attach_database('estgene', $estgene_db);

  Description: Attaches a database to the seqdumper that can be used to 
               dump data which is external to the ensembl core database.
               Currently this is necessary to dump est genes and vega genes
  Returntype : none
  Exceptions : thrown if incorrect argument is supplied
  Caller     : general

Code:

click to view

◆ disable_feature_type()

public void Bio::EnsEMBL::Utils::SeqDumper::disable_feature_type ( )

  Arg [1]    : string $type
  Example    :

$seq_dumper->disable_feature_type('genes');

  Description: Disables the dumping of a specific type of feature
  Returntype : none
  Exceptions : warn if an invalid feature type is passed,
               thrown if no feature type is passed
  Caller     : general

Code:

click to view

◆ dump()

public void Bio::EnsEMBL::Utils::SeqDumper::dump ( )

  Arg [1]    : Bio::EnsEMBL::Slice slice
               The slice to dump
  Arg [2]    : string $format
               The name of the format to dump
  Arg [3]    : (optional) $outfile
               The name of the file to dump to. If no file is specified STDOUT
               is used
  Arg [4]    : (optional) $seq
               Sequence to dump
  Arg [4]    : (optional) $no_append
               Default action is to open the file in append mode. This will
               turn that mode off
  Example    :

$seq_dumper->dump($slice, 'EMBL');

  Description: Dumps a region of a genome specified by the slice argument into
               an outfile of the format $format
  Returntype : none
  Exceptions : thrown if slice or format args are not supplied
  Caller     : general

Code:

click to view

◆ dump_embl()

public void Bio::EnsEMBL::Utils::SeqDumper::dump_embl ( )

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : IO::File $FH
  Arg [3]    : optional sequence string
  Example    :

$seq_dumper->dump_embl($slice, $FH);

  Description: Dumps an EMBL flat file to an open file handle
  Returntype : none
  Exceptions : if calls to get/set the filehandle position fail
  Caller     : dump

Code:

click to view

sub dump_embl {
  my $self = shift;
  my $slice = shift;
  my $FH   = shift;
 
  my $len = $slice->length;
 
  my $version;
  my $acc;
 
  my $cs = $slice->coord_system();
  my $name_str = $cs->name() . ' ' . $slice->seq_region_name();
  $name_str .= ' ' . $cs->version if($cs->version);
 
  my $start = $slice->start;
  my $end   = $slice->end;
 
  #determine if this slice is the entire seq region
  #if it is then we just use the name as the id
  my $slice_adaptor = $slice->adaptor();
  my $full_slice =
    $slice->adaptor->fetch_by_region($cs->name,
                                    $slice->seq_region_name,
                                    undef,undef,undef,
                                    $cs->version);
 
  my $entry_name = $slice->seq_region_name();
 
  if($full_slice->name eq $slice->name) {
    $name_str .= ' full sequence';
    $acc = $slice->seq_region_name();
    my @acc_ver = split(/\./, $acc);
    if(@acc_ver == 2) {
      $acc = $acc_ver[0];
      $version = $acc_ver[0] . '.'. $acc_ver[1];
    } elsif(@acc_ver == 1 && $cs->version()) {
      $version = $acc . '.'. $cs->version();
    } else {
      $version = $acc;
    }
  } else {
    $name_str .= ' partial sequence';
    $acc = $slice->name();
    $version = $acc;
  }
 
  $acc = $slice->name();
 
  #line breaks are allowed near the end of the line on ' ', "\t", "\n", ',' 
  $: = (" \t\n-,");
 
  #############
  # dump header
  #############
 
  # move at the end of file in case the file
  # is open more than once (i.e. human chromosome Y, 
  # two chromosome slices
  #
  # WARNING
  #
  # When the file is open not for the first time,
  # it must be in read/write mode
  #
  seek($FH, 0, SEEK_END);
 
  my $EMBL_HEADER = 
'@<   ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~
';
 
  #ID and moltype
  # HTG = High Throughput Genome division, probably most suitable
  #       and it would be hard to come up with another appropriate division
  #       that worked for all organisms (e.g. plants are in PLN but human is
  #       in HUM).
  my $VALUE = "$entry_name    standard; DNA; HTG; $len BP.";
  $self->write($FH, $EMBL_HEADER, 'ID', $VALUE);  
  $self->print( $FH, "XX\n" );
 
  #Accession
  $self->write($FH, $EMBL_HEADER, 'AC', $acc);
  $self->print( $FH, "XX\n" );
 
  #Version
  $self->write($FH, $EMBL_HEADER, 'SV', $version);
  $self->print( $FH, "XX\n" );
 
  #Date
  $self->write($FH, $EMBL_HEADER, 'DT', $self->_date_string);
  $self->print( $FH, "XX\n" );
 
  my $meta_container = $slice->adaptor()->db()->get_MetaContainer();
  
  #Description
  $self->write($FH, $EMBL_HEADER, 'DE', $meta_container->get_scientific_name() .
               " $name_str $start..$end annotated by Ensembl");
  $self->print( $FH, "XX\n" );
 
  #key words
  $self->write($FH, $EMBL_HEADER, 'KW', '.');
  $self->print( $FH, "XX\n" );
 
  #Species
  my $species_name = $meta_container->get_scientific_name();
  if(my $cn = $meta_container->get_common_name()) {
    $species_name .= " ($cn)";
  }
 
  $self->write($FH, $EMBL_HEADER, 'OS', $species_name);
 
  #Classification
  my @cls = @{$meta_container->get_classification()};
  $self->write($FH, $EMBL_HEADER, 'OC', join('; ', reverse(@cls)) . '.');
  $self->print( $FH, "XX\n" );
  
  #References (we are not dumping refereneces)
  #Database References (we are not dumping these)
 
  #comments
  my $annotation_source = $self->annotation_source($meta_container);
  foreach my $comment (@COMMENTS) {
    $comment =~ s/\#\#\#SOURCE\#\#\#/$annotation_source/;
    $self->write($FH, $EMBL_HEADER, 'CC', $comment);
    $self->print( $FH, "XX\n" );
  }
 
  ####################
  # DUMP FEATURE TABLE
  ####################
  $self->print( $FH, "FH   Key             Location/Qualifiers\n" );
 
  my $FEATURE_TABLE = 
'FT   ^<<<<<<<<<<<<<<<^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~
';
  $self->_dump_feature_table($slice, $FH, $FEATURE_TABLE);  
 
  #write an XX after the feature tables
  $self->print( $FH, "XX\n" );
 
  ###################
  # DUMP SEQUENCE
  ###################
 
  # record position before writing sequence header, so that 
  # after printing the sequence and having the base counts
  # we can seek to this position and write the proper sequence 
  # header
  my $sq_offset = tell($FH);
  $sq_offset == -1 and throw "Unable to get offset for output fh";
 
  # print a sequence header template, to be replaced with a real
  # one containing the base counts
  $self->print($FH, "SQ   Sequence ########## BP; ########## A; ########## C; ########## G; ########## T; ########## other;\n");
  
  # dump the sequence and get the base counts
  my $acgt = $self->write_embl_seq($slice, $FH);
  
  # print the end of EMBL entry
  $self->print( $FH, "//\n" );
  my $end_of_entry_offset = tell($FH);
  $end_of_entry_offset == -1 and throw "Unable to get offset for output fh";
 
  # seek backwards to the position of the sequence header and 
  # write it with the actual base counts
  seek($FH, $sq_offset, SEEK_SET) 
    or throw "Cannot seek backward to sequence header position";
  $self->print($FH, sprintf "SQ   Sequence %10d BP; %10d A; %10d C; %10d G; %10d T; %10d other;", 
           $acgt->{tot}, $acgt->{a}, $acgt->{c}, $acgt->{g}, $acgt->{t}, $acgt->{n});
 
  # move forward to end of file to dump the next slice
  seek($FH, $end_of_entry_offset, SEEK_SET) 
    or throw "Cannot seek forward to end of entry";
 
  # Set formatting back to normal
  $: = " \n-";
}

◆ dump_fasta()

public void Bio::EnsEMBL::Utils::SeqDumper::dump_fasta ( )

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : IO::File $FH
  Example    :

$seq_dumper->dump_fasta($slice, $FH);

  Description: Dumps an FASTA flat file to an open file handle
  Returntype : none
  Exceptions : none
  Caller     : dump

Code:

click to view

◆ dump_genbank()

public void Bio::EnsEMBL::Utils::SeqDumper::dump_genbank ( )

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : IO::File $FH
  Example    :

$seq_dumper->dump_genbank($slice, $FH);

  Description: Dumps a GENBANK flat file to an open file handle
  Returntype : none
  Exceptions : none
  Caller     : dump

Code:

click to view

sub dump_genbank {
  my ($self, $slice, $FH) = @_;
 
  #line breaks are allowed near the end of the line on ' ', "\t", "\n", ',' 
  $: = " \t\n-,";
 
  my $GENBANK_HEADER = 
'^<<<<<<<<<  ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~~
';
 
  my $GENBANK_SUBHEADER =
'  ^<<<<<<<  ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~~
';
 
  my $GENBANK_FT =
'     ^<<<<<<<<<<<<<< ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~~
';
 
  my $version;
  my $acc;
 
  my $cs = $slice->coord_system();
 
  my $name_str = $cs->name() . ' ' . $slice->seq_region_name();
 
  $name_str .= ' ' . $cs->version if($cs->version);
 
  #determine if this slice is the entire seq region
  #if it is then we just use the name as the id
  my $slice_adaptor = $slice->adaptor();
  my $full_slice =
    $slice->adaptor->fetch_by_region($cs->name,
                                    $slice->seq_region_name,
                                    undef,undef,undef,
                                    $cs->version);
 
 
  my $entry_name = $slice->seq_region_name();
 
  if($full_slice->name eq $slice->name) {
    $name_str .= ' full sequence';
    $acc = $slice->seq_region_name();
    my @acc_ver = split(/\./, $acc);
    if(@acc_ver == 2) {
      $acc = $acc_ver[0];
      $version = $acc_ver[0] . $acc_ver[1];
    } elsif(@acc_ver == 1 && $cs->version()) {
      $version = $acc . $cs->version();
    } else {
      $version = $acc;
    }
  } else {
    $name_str .= ' partial sequence';
    $acc = $slice->name();
    $version = $acc;
  }
 
  $acc = $slice->name();     # to keep format consistent for all
 
  my $length = $slice->length;
  my $start = $slice->start();
  my $end   = $slice->end();
 
  my $date = $self->_date_string;
 
  my $meta_container = $slice->adaptor()->db()->get_MetaContainer();
 
  # move at the end of file in case the file
  # is open more than once (i.e. human chromosome Y, 
  # two chromosome slices
  #
  # WARNING
  #
  # When the file is open not for the first time,
  # it must be in read/write mode
  #
  seek($FH, 0, SEEK_END);
 
  #LOCUS
  my $tag   = 'LOCUS';
  my $value = "$entry_name $length bp DNA HTG $date";
  $self->write($FH, $GENBANK_HEADER, $tag, $value);
 
  #DEFINITION
  $tag   = "DEFINITION";
  $value = $meta_container->get_scientific_name() . 
    " $name_str $start..$end reannotated via EnsEMBL";
  $self->write($FH, $GENBANK_HEADER, $tag, $value);
 
  #ACCESSION
  $self->write($FH, $GENBANK_HEADER, 'ACCESSION', $acc);
 
  #VERSION
  $self->write($FH, $GENBANK_HEADER, 'VERSION', $version);
 
  # KEYWORDS
  $self->write($FH, $GENBANK_HEADER, 'KEYWORDS', '.');
 
  # SOURCE
  my $common_name = $meta_container->get_common_name();
  $common_name = $meta_container->get_scientific_name() unless $common_name;
  $self->write($FH, $GENBANK_HEADER, 'SOURCE', $common_name);
 
  #organism
  my @cls = @{$meta_container->get_classification()};
  shift @cls;
  $self->write($FH, $GENBANK_SUBHEADER, 'ORGANISM', $meta_container->get_scientific_name());
  $self->write($FH, $GENBANK_SUBHEADER, '', join('; ', reverse @cls) . ".");
 
  #refereneces
 
  #comments
  my $annotation_source = $self->annotation_source($meta_container);
  foreach my $comment (@COMMENTS) {
    $comment =~ s/\#\#\#SOURCE\#\#\#/$annotation_source/;
    $self->write($FH, $GENBANK_HEADER, 'COMMENT', $comment);
  }
 
  ####################
  # DUMP FEATURE TABLE
  ####################
  $self->print( $FH, "FEATURES             Location/Qualifiers\n" );
  $self->_dump_feature_table($slice, $FH, $GENBANK_FT);
 
  ####################
  # DUMP SEQUENCE
  ####################
 
  # record position before writing sequence header, so that 
  # after printing the sequence and having the base counts
  # we can seek to this position and write the proper sequence 
  # header
  my $sq_offset = tell($FH);
  $sq_offset == -1 and throw "Unable to get offset for output fh";
 
  # print a sequence header template, to be replaced with a real
  # one containing the base counts
  $self->print($FH, "BASE COUNT  ########## a ########## c ########## g ########## t ########## n\nORIGIN\n");
  
  # dump the sequence and get the base counts
  my $acgt = $self->write_genbank_seq($slice, $FH);
  
  # print the end of genbank entry
  $self->print( $FH, "//\n" );
  my $end_of_entry_offset = tell($FH);
  $end_of_entry_offset == -1 and throw "Unable to get offset for output fh";
 
  # seek backwards to the position of the sequence header and 
  # write it with the actual base counts
  seek($FH, $sq_offset, SEEK_SET) 
    or throw "Cannot seek backward to sequence header position";
  $self->print($FH, sprintf "BASE COUNT  %10d a %10d c %10d g %10d t %10d n", 
           $acgt->{a}, $acgt->{c}, $acgt->{g}, $acgt->{t}, $acgt->{n});
 
  seek($FH, $end_of_entry_offset, SEEK_SET) 
    or throw "Cannot seek forward to end of entry";
 
  # Set formatting back to normal
  $: = " \n-";
}

◆ enable_feature_type()

public void Bio::EnsEMBL::Utils::SeqDumper::enable_feature_type ( )

  Arg [1]    : string $type
  Example    :

$seq_dumper->enable_feature_type('similarity');

  Description: Enables the dumping of a specific type of feature
  Returntype : none
  Exceptions : warn if invalid feature type is passed,
               thrown if no feature type is passed
  Caller     : general

Code:

click to view

◆ features2location()

public String Bio::EnsEMBL::Utils::SeqDumper::features2location ( )

  Arg [1]    : listref of Bio::EnsEMBL::SeqFeatures
  Example    :

$location = $self->features2location(\@features);

  Description: Constructs an EMBL location string from a list of features
  Returntype : string
  Exceptions : none
  Caller     : internal

Code:

click to view

◆ get_database()

public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::Utils::SeqDumper::get_database ( )

  Arg [1]    : string $name
  Example    :

$db = $seq_dumper->get_database('vega');

  Description: Retrieves a database that has been attached to the 
               seqdumper via the attach database call.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : thrown if incorrect argument is supplied
  Caller     : dump_feature_table

Code:

click to view

◆ is_enabled()

public void Bio::EnsEMBL::Utils::SeqDumper::is_enabled ( )

  Arg [1]    : string $type 
  Example    :

do_something() if($seq_dumper->is_enabled('gene'));

  Description: checks if a specific feature type is enabled
  Returntype : none
  Exceptions : warning if invalid type is passed, 
               thrown if no type is passed 
  Caller     : general

Code:

click to view

◆ new()

public Bio::EnsEMBL::Utils::SeqDumper Bio::EnsEMBL::Utils::SeqDumper::new ( )

  Arg [1]    : none
  Example    :

$seq_dumper = Bio::EnsEMBL::Utils::SeqDumper->new;

  Description: Creates a new SeqDumper 
  Returntype : Bio::EnsEMBL::Utils::SeqDumper
  Exceptions : none
  Caller     : general

Code:

click to view

◆ print()

public Bio::EnsEMBL::Utils::SeqDumper::print ( )

Undocumented method

Code:

click to view

◆ remove_database()

public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::Utils::SeqDumper::remove_database ( )

  Arg [1]    : string $name 
  Example    :

$db = $seq_dumper->remove_database('estgene');

  Description: Removes a database that has been attached to the seqdumper
               via the attach database call.  The database that is removed
               is returned (or undef if it did not exist).
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : thrown if incorrect argument is supplied
  Caller     : general

Code:

click to view

◆ transcript_to_codon_start()

public Bio::EnsEMBL::Utils::SeqDumper::transcript_to_codon_start ( )

Undocumented method

Code:

click to view

◆ write()

public Bio::EnsEMBL::Utils::SeqDumper::write ( )

Undocumented method

Code:

click to view

◆ write_embl_seq()

public Bio::EnsEMBL::Utils::SeqDumper::write_embl_seq ( )

Undocumented method

Code:

click to view

◆ write_genbank_seq() [1/2]

public Bio::EnsEMBL::Utils::SeqDumper::write_genbank_seq ( )

Undocumented method

Code:

click to view

Undocumented method

Code:

click to view

◆ write_genbank_seq() [2/2]

public Bio::EnsEMBL::Utils::SeqDumper::write_genbank_seq ( )

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/Utils/SeqDumper.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _date_string()

◆ _dump_feature_table()

◆ _get_codon_table_id()

◆ annotation_source()

◆ attach_database()

◆ disable_feature_type()

◆ dump()

◆ dump_embl()

◆ dump_fasta()

◆ dump_genbank()

◆ enable_feature_type()

◆ features2location()

◆ get_database()

◆ is_enabled()

◆ new()

◆ print()

◆ remove_database()

◆ transcript_to_codon_start()

◆ write()

◆ write_embl_seq()

◆ write_genbank_seq() [1/2]

◆ write_genbank_seq() [2/2]