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Bio-EnsEMBL-113_51
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/ 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