.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::exonerate 3pm"
.TH Bio::SearchIO::exonerate 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::SearchIO::exonerate \- parser for Exonerate
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # do not use this module directly, it is a driver for SearchIO
\&
\&  use Bio::SearchIO;
\&  my $searchio = Bio::SearchIO\->new(\-file => \*(Aqfile.exonerate\*(Aq,
\&                                   \-format => \*(Aqexonerate\*(Aq);
\&
\&
\&  while( my $r = $searchio\->next_result ) {
\&    print $r\->query_name, "\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a driver for the SearchIO system for parsing Exonerate (Guy
Slater) output.  You can get Exonerate at
http://www.ebi.ac.uk/~guy/exonerate/
[until Guy puts up a Web reference,publication for it.]).
.PP
An optional parameter \-min_intron is supported by the new
initialization method.  This is if you run Exonerate with a different
minimum intron length (default is 30) the parser will be able to
detect the difference between standard deletions and an intron.  Still
some room to play with there that might cause this to get
misinterpreted that has not been fully tested or explored.
.PP
The \s-1VULGAR\s0 and \s-1CIGAR\s0 formats should be parsed okay now creating HSPs
where appropriate (so merging match states where appropriate rather
than breaking an \s-1HSP\s0 at each indel as it may have done in the past).
The \s-1GFF\s0 that comes from exonerate is still probably a better way to go
if you are doing protein2genome or est2genome mapping.
For example you can see this script:
.PP
### \s-1TODO:\s0 Jason, this link is dead, do we have an updated one?
http://fungal.genome.duke.edu/~jes12/software/scripts/process_exonerate_gff3.perl.txt
.PP
If your report contains both \s-1CIGAR\s0 and \s-1VULGAR\s0 lines only the first one
will processed for a given Query/Target pair.  If you preferentially
want to use \s-1VULGAR\s0 or \s-1CIGAR\s0 add one of these options when initializing
the SearchIO object.
.PP
.Vb 3
\&    \-cigar  => 1
\&OR
\&    \-vulgar => 1
.Ve
.PP
Or set them via these methods.
.PP
.Vb 3
\&    $parser\->cigar(1)
\&OR
\&    $parser\->vulgar(1)
.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 \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : my $obj = Bio::SearchIO::exonerate\->new();
\& Function: Builds a new Bio::SearchIO::exonerate object
\& Returns : an instance of Bio::SearchIO::exonerate
\& Args    : \-min_intron => somewhat obsolete option, how to determine if a
\&                          an indel is an intron or a local gap.  Use VULGAR
\&                          rather than CIGAR to avoid this heuristic,default 30.
\&           \-cigar       => 1   set this to 1 if you want to parse
\&                               CIGAR exclusively.
\&           \-vulgar      => 1   set this to 1 if you want to parse VULGAR
\&                               exclusively, setting both to 1 will revert
\&                               to the default behavior of just parsing the
\&                               first line that it sees.
.Ve
.SS "next_result"
.IX Subsection "next_result"
.Vb 5
\& Title   : next_result
\& Usage   : my $hit = $searchio\->next_result;
\& Function: Returns the next Result from a search
\& Returns : Bio::Search::Result::ResultI object
\& Args    : none
.Ve
.SS "start_element"
.IX Subsection "start_element"
.Vb 5
\& Title   : start_element
\& Usage   : $eventgenerator\->start_element
\& Function: Handles a start element event
\& Returns : none
\& Args    : hashref with at least 2 keys \*(AqData\*(Aq and \*(AqName\*(Aq
.Ve
.SS "end_element"
.IX Subsection "end_element"
.Vb 5
\& Title   : start_element
\& Usage   : $eventgenerator\->end_element
\& Function: Handles an end element event
\& Returns : none
\& Args    : hashref with at least 2 keys \*(AqData\*(Aq and \*(AqName\*(Aq
.Ve
.SS "element"
.IX Subsection "element"
.Vb 5
\& Title   : element
\& Usage   : $eventhandler\->element({\*(AqName\*(Aq => $name, \*(AqData\*(Aq => $str});
\& Function: Convience method that calls start_element, characters, end_element
\& Returns : none
\& Args    : Hash ref with the keys \*(AqName\*(Aq and \*(AqData\*(Aq
.Ve
.SS "characters"
.IX Subsection "characters"
.Vb 5
\& Title   : characters
\& Usage   : $eventgenerator\->characters($str)
\& Function: Send a character events
\& Returns : none
\& Args    : string
.Ve
.SS "within_element"
.IX Subsection "within_element"
.Vb 7
\& Title   : within_element
\& Usage   : if( $eventgenerator\->within_element($element) ) {}
\& Function: Test if we are within a particular element
\&           This is different than \*(Aqin\*(Aq because within can be tested
\&           for a whole block.
\& Returns : boolean
\& Args    : string element name
.Ve
.SS "in_element"
.IX Subsection "in_element"
.Vb 7
\& Title   : in_element
\& Usage   : if( $eventgenerator\->in_element($element) ) {}
\& Function: Test if we are in a particular element
\&           This is different than \*(Aqin\*(Aq because within can be tested
\&           for a whole block.
\& Returns : boolean
\& Args    : string element name
.Ve
.SS "start_document"
.IX Subsection "start_document"
.Vb 5
\& Title   : start_document
\& Usage   : $eventgenerator\->start_document
\& Function: Handle a start document event
\& Returns : none
\& Args    : none
.Ve
.SS "end_document"
.IX Subsection "end_document"
.Vb 5
\& Title   : end_document
\& Usage   : $eventgenerator\->end_document
\& Function: Handles an end document event
\& Returns : Bio::Search::Result::ResultI object
\& Args    : none
.Ve
.SS "vulgar"
.IX Subsection "vulgar"
.Vb 5
\& Title   : vulgar
\& Usage   : $obj\->vulgar($newval)
\& Function: Get/Set flag, do you want to build HSPs from VULGAR string?
\& Returns : value of vulgar (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve
.SS "cigar"
.IX Subsection "cigar"
.Vb 5
\& Title   : cigar
\& Usage   : $obj\->cigar($newval)
\& Function: Get/Set boolean flag do you want to build HSPs from CIGAR strings?
\& Returns : value of cigar (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve