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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::megablast 3pm"
.TH Bio::SearchIO::megablast 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.
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.nh
.SH "NAME"
Bio::SearchIO::megablast \- a driver module for Bio::SearchIO to parse
megablast reports (format 0)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
# do not use this module directly
.PP
.Vb 5
\&  use Bio::SearchIO;
\&  # for default format output from megablast
\&  my $in = Bio::SearchIO\->new(\-file   => \*(Aqfile.mbl\*(Aq,
\&                             \-format => \*(Aqmegablast\*(Aq,
\&                             \-report_format => 0);
\&
\&  while( my $r = $in\->next_result ) {
\&    while( my $hit = $r\->next_hit ) {
\&      while( my $hsp = $hit\->next_hsp ) {
\&      }
\&    }
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Beware!
.PP
Because of the way megablast report format 0 is coded, realize that score
means # gap characters + # mismatches for a \s-1HSP.\s0
.PP
The docs from \s-1NCBI\s0 regarding \s-1FORMAT 0\s0
#   0: Produce one-line output for each alignment, in the form
#
#   'subject\-id'=='[+\-]query\-id' (s_off q_off s_end q_end) score
#
#   Here subject(query)\-id is a gi number, an accession or some other type of
#   identifier found in the \s-1FASTA\s0 definition line of the respective sequence.
#
#   + or \- corresponds to same or different strand alignment.
#
#   Score for non-affine gapping parameters means the total number of
#   differences (mismatches + gap characters). For affine case it is the
#   actual (raw) score of the alignment.
.PP
\&\s-1FORMAT 1\s0 parsing has not been implemented
\&\s-1FORMAT 2\s0 parsing should work with the SearchIO 'blast' parser
.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 6
\& Title   : new
\& Usage   : my $obj = Bio::SearchIO::blast\->new();
\& Function: Builds a new Bio::SearchIO::blast object
\& Returns : Bio::SearchIO::blast
\& Args    : \-fh/\-file => filehandle/filename to BLAST file
\&           \-format   => \*(Aqblast\*(Aq
.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 "report_format"
.IX Subsection "report_format"
.Vb 5
\& Title   : report_format
\& Usage   : $obj\->report_format($newval)
\& Function: Get/Set the report_format value
\& Returns : value of report_format (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.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 "_mode"
.IX Subsection "_mode"
.Vb 6
\& Title   : _mode
\& Usage   : $obj\->_mode($newval)
\& Function:
\& Example :
\& Returns : value of _mode
\& Args    : newvalue (optional)
.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: Handles 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 "result_count"
.IX Subsection "result_count"
.Vb 5
\& Title   : result_count
\& Usage   : my $count = $searchio\->result_count
\& Function: Returns the number of results we have processed
\& Returns : integer
\& Args    : none
.Ve