.\" 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 "RG::Blast::Parser 3pm"
.TH RG::Blast::Parser 3pm "2020-11-27" "perl v5.32.0" "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"
RG::Blast::Parser \- fast NCBI BLAST parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  use Data::Dumper;
\&  use RG::Blast::Parser;
\&
\&  my $parser = RG::Blast::Parser\->new(); # read from STDIN
\&
\&  open( EXAMPLE, \*(Aq<\*(Aq, \*(Aq/usr/share/doc/librg\-blast\-parser\-perl/examples/converged.ali\*(Aq ) || confess($!);
\&  my $parser = RG::Blast::Parser\->new( \e*EXAMPLE, "converged.ali" ); # read from EXAMPLE, use name "converged.ali" in error messages
\&
\&  while( my $res = $parser\->parse() )
\&  {
\&    print Dumper( $res );
\&  }
\&
\&  eval {
\&    my $res = $parser\->parse();
\&    # ...
\&  };
\&  if( $@ && $@ =~ /^parser error/ ) { warn("failed to parse blast result \- exception caught"); }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This package contains perl binding for a very fast C/\*(C+ library for \s-1NCBI
BLAST\s0 \-m 0 (default) output parsing.  \s-1BLAST\s0 results are returned in a
convenient hash structure.
.PP
Multiple results may be concatenated for input.  One result is parsed and
returned at a time.
.SH "CONSTRUCTOR"
.IX Header "CONSTRUCTOR"
.IP "new( [\s-1FILEHANDLE,\s0 [\s-1NAME\s0]] )" 4
.IX Item "new( [FILEHANDLE, [NAME]] )"
Creates an \*(L"RG::Blast::Parser\*(R".  Blast results are read from \s-1FILEHANDLE, STDIN\s0
by default.  The input stream may be named \s-1NAME\s0 in error messages (default:
\&\*(L"\s-1STDIN\*(R"\s0).
.SH "METHODS"
.IX Header "METHODS"
.IP "parse( [\s-1TRACE_PARSING,\s0 [\s-1TRACE_SCANNING\s0]] )" 4
.IX Item "parse( [TRACE_PARSING, [TRACE_SCANNING]] )"
Parse one complete \s-1BLAST\s0 result and return it.  If no results on input stream,
returns \*(L"undef\*(R".  In case of parser error it \fBdie()\fRs with an (at present not
very useful) error message.
.Sp
The following structure is returned in a hash reference:
.Sp
.Vb 10
\&  {
\&    blast_version =>    STRING,
\&    references =>       [ STRING, ... ],
\&    rounds => [
\&        {
\&            oneline_idx =>      NUM,    # index of first one\-line description of
\&                                        # this round in "onelines" array
\&            oneline_cnt =>      NUM,    # number of one\-line descriptions of
\&                                        # this round
\&            hit_idx =>          NUM,    # index of first hit of this round in
\&                                        # "hits" array
\&            hit_cnt =>          NUM,    # number of hits of this round
\&            oneline_new_idx =>  NUM|undef# index of first new (not\-seen\-before)
\&                                        # one\-line description of this round
\&                                        # in "onelines" array
\&            oneline_new_cnt =>  NUM     # number of new one\-line descriptions of
\&                                        # this round
\&        }, ...
\&    ],
\&    q_name =>       STRING,
\&    q_desc =>       STRING|undef,
\&    q_length =>     NUM,
\&    db_name =>      STRING,
\&    db_nseq =>      NUM,
\&    db_nletter =>   NUM,
\&    onelines =>     [                   # one\-line descriptions from all rounds
\&        {
\&            name =>         STRING,
\&            desc =>         STRING|undef,
\&            bit_score =>    NUM,
\&            e_value =>      NUM
\&        }, ...
\&    ],
\&    converged =>    BOOLEAN,
\&    hits =>         [                   # hits from all rounds
\&        {
\&            name =>         STRING,
\&            desc =>         STRING|undef,
\&            length =>       NUM,
\&            hsps =>         [
\&                {
\&                    bit_score =>    NUM,
\&                    raw_score =>    NUM,
\&                    e_value =>      NUM,
\&                    method =>       STRING,
\&                    identities =>   NUM,
\&                    positives =>    NUM,
\&                    gaps =>         NUM,
\&                    q_strand =>     STRING|undef,
\&                    s_strand =>     STRING|undef,
\&                    q_frame =>      NUM|undef,
\&                    s_frame =>      NUM|undef,
\&                    q_start =>      NUM,
\&                    q_ali =>        STRING,
\&                    q_end =>        NUM,
\&                    match_line =>   STRING,
\&                    s_start =>      NUM,
\&                    s_ali =>        STRING,
\&                    s_end =>        NUM
\&                }, ...
\&            ]
\&        }, ...
\&    ],
\&    tail =>         STRING              # bulk text after the last hit / one\-line
\&                                        # description
\&  }
.Ve
.Sp
If you want tracing for parsing and scanning, you can enable them using the
parameters of this call.
.IP "\fBresult()\fR" 4
.IX Item "result()"
Returns the last \s-1BLAST\s0 result parsed or \*(L"undef\*(R" if no last result.
.IP "\fBget_trace_scanning()\fR" 4
.IX Item "get_trace_scanning()"
Returns scan trace state as a Boolean value.
.IP "set_trace_scanning( \s-1BOOLEAN\s0 )" 4
.IX Item "set_trace_scanning( BOOLEAN )"
Set scan trace \- debugging aid.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBZerg\fR\|(3pm), \fBZerg::Report\fR\|(3pm)
.SH "AUTHOR"
.IX Header "AUTHOR"
Laszlo Kajan, <lkajan@rostlab.org>
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
Copyright (C) 2012 by Laszlo Kajan
.PP
This program is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.8 or,
at your option, any later version of Perl 5 you may have available.