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.\" ========================================================================
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.IX Title "Bio::SeqIO::entrezgene 3pm"
.TH Bio::SeqIO::entrezgene 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::SeqIO::entrezgene \- Entrez Gene ASN1 parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&   use Bio::SeqIO;
\&
\&   # don\*(Aqt instantiate directly \- instead do
\&   my $seqio = Bio::SeqIO\->new(\-format => \*(Aqentrezgene\*(Aq,
\&                               \-file => $file);
\&   my $gene = $seqio\->next_seq;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is EntrezGene \s-1ASN\s0 bioperl parser. It is built on top of 
Bio::ASN1::EntrezGene, a low level \s-1ASN\s0 parser built by Mingyi Liu 
(<http://sourceforge.net/projects/egparser>). The easiest way to 
use it is shown above.
.PP
You will get most of the Entrez Gene annotation such as gene symbol, 
gene name and description, accession numbers associated 
with the gene, etc. Almost all of these are given as  Bio::AnnotationI objects.
.PP
If you need all the data do:
.PP
.Vb 4
\&   my $seqio = Bio::SeqIO\->new(\-format => \*(Aqentrezgene\*(Aq,
\&                               \-file => $file,
\&                               \-debug => \*(Aqon\*(Aq );
\&   my ($gene,$genestructure,$uncaptured) = $seqio\->next_seq;
.Ve
.PP
The second variable returned, \f(CW$genestructure\fR, is a Bio::Cluster::SequenceFamily
object. It contains all Refseqs and the genomic contigs that are associated 
with the particular gene. The third variable, \f(CW$uncaptured\fR, is a reference 
to a plain array.
.PP
You can also modify the output to allow back compatibility with the old 
LocusLink parser:
.PP
.Vb 3
\&   my $seqio = Bio::SeqIO\->new(\-format => \*(Aqentrezgene\*(Aq,
\&                               \-file => $file,
\&                               \-locuslink => \*(Aqconvert\*(Aq);
.Ve
.PP
The \f(CW\*(C`\-debug\*(C'\fR and \f(CW\*(C`\-locuslink\*(C'\fR options slow down the parser.
.PP
Example code which looks for ontology terms:
.PP
.Vb 3
\&  my $eio = new Bio::SeqIO(\-file => $file,
\&                           \-format => \*(Aqentrezgene\*(Aq,
\&                           \-service_record => \*(Aqyes\*(Aq);
\&
\&  while (my $seq = $eio\->next_seq) {
\&    my $gid = $seq\->accession_number;
\&    foreach my $ot ($ann\->get_Annotations(\*(AqOntologyTerm\*(Aq)) {
\&      next if ($ot\->term\->authority eq \*(AqSTS marker\*(Aq); # No STS markers
\&      my $evid = $ot\->comment;
\&      $evid =~ s/evidence: //i;
\&      my @ref = $ot\->term\->get_references;
\&      my $id = $ot\->identifier;
\&      my $fid = \*(AqGO:\*(Aq . sprintf("%07u",$id);
\&      print join("\et",$gid, $ot\->ontology\->name, $ot\->name, $evid,
\&        $fid, @ref?$ref[0]\->medline:\*(Aq\*(Aq), "\en";
\&    }
\&  }
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Stefan Kirov"
.IX Header "AUTHOR - Stefan Kirov"
Email skirov at utk.edu
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Hilmar Lapp, hlapp at gmx.net
.SH "APPENDIX"
.IX Header "APPENDIX"
This parser is based on Bio::ASN1::EntrezGene module.
.PP
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SH "_process_products_coordinates"
.IX Header "_process_products_coordinates"
To do:
.SH "_process_prop"
.IX Header "_process_prop"
To do: process \s-1GO\s0