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Bio-EnsEMBL-112.0.0_57
River stage zero No dependents
/ Bio::EnsEMBL::Utils::SeqDumper

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::Utils::SeqDumper

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.

METHODS

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

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

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

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

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

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

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

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

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

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

_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

_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

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

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

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