zerg::report(3pm) [debian man page]

Report(3pm)						User Contributed Perl Documentation					       Report(3pm)

NAME

       Zerg::Report - get attributes from a BLAST file in a data structure

SYNOPSIS

	 use Zerg::Report;

	 my $zerg_report = new Zerg::Report("output.blastn");

	 while($r=$zerg_report->getReport())
	 {
	   foreach my $hit (@{$r->{hits}})
	   {
	     foreach my $hsp (@{$hit->{hsps}})
	     {
	       print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}
";
	     }
	   }
	 }

	 $zerg_report->closeFile();

DESCRIPTION

	 Zerg::Report uses Zerg to parse a file - or STDIN if file is not given -
	 containing one or multiple BLAST reports and, for each report, stores
	 the obtained fields in a data structure made of arrays and hashes.
	 Please consult the Zerg man page to see which fields are extracted.

	 The method getReport() reads a BLAST report from the input file and
	 returns a reference to a data structure like the one in the example
	 below. When no report is found, it returns undef. It dies from
	 syntax errors in BLAST reports with a stack backtrace.

	 Example of a data structure returned by getReport():

	 $r = {
		 'query_name' => 'ME1-0081T-R227-B12-U.G',
		 'blast_version' => 'BLASTX 1.3.6 [2002-03-05]',
		 'byte_offset' => 4981,
		 'query_length' => '444',
		 'query_annotation' => ''
		 'round_begins' => [ 0, 129, 201 ], # indicates the first hit in each round of iterated blast
		 'hits' => [
			     {
			       'subject_annotation' => '(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD-e]',
			       'hsps' => [
					   {
					     'query_end' => '82',
					     'subject_ali' => 'ASELEIFAALIECEA-GSTDYDGMLAVASVVMNRVNHRYYPDTITGVIYQSGQFSPVASGKLDKVLKRGIKSSCLEVAKDA',
					     'query_ali' => 'DAQTRKLAAIAYGEASGANDANEIGGIAWAVANRARAWGGK-TVDGLLAADPNYTYAVKDG-NQRYAKLMKATEAAIAADP',
					     'subject_end' => '328',
					     'identities' => '15',
					     'score' => '87',
					     'percent_positives' => '41',
					     'gaps' => '3',
					     'score_bits' => '37.9',
					     'alignment_length' => '81',
					     'evalue' => '0.40',
					     'percent_identities' => '18',
					     'positives' => '34',
					     'query_start' => '4',
					     'subject_start' => '249'
					   }
					 ],
			       'subject_length' => '880',
			       'subject_name' => 'gi|16802882|ref|NP_464367.1|'
			     },
			   ],
	       };

AUTHORS

       Apua~ Paquola <apua@iq.usp.br>, Abimael Machado <abimael@iq.usp.br> IQ-USP Bioinformatics Lab

       Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich

SEE ALSO

       Zerg

perl v5.14.2							    2011-11-15							       Report(3pm)

RG::Blast::Parser(3pm)					User Contributed Perl Documentation				    RG::Blast::Parser(3pm)

NAME

       RG::Blast::Parser - fast NCBI BLAST parser

SYNOPSIS

	 use Data::Dumper;
	 use RG::Blast::Parser;

	 my $parser = RG::Blast::Parser->new(); # read from STDIN

	 open( EXAMPLE, '<', '/usr/share/doc/librg-blast-parser-perl/examples/converged.ali' ) || confess($!);
	 my $parser = RG::Blast::Parser->new( *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"); }

DESCRIPTION

       This package contains perl binding for a very fast C/C++ library for NCBI BLAST -m 0 (default) output parsing.  BLAST results are returned
       in a convenient hash structure.

       Multiple results may be concatenated for input.	One result is parsed and returned at a time.

CONSTRUCTOR

       new( [FILEHANDLE, [NAME]] )
	   Creates an "RG::Blast::Parser".  Blast results are read from FILEHANDLE, STDIN by default.  The input stream may be named NAME in error
	   messages (default: "STDIN").

METHODS

       parse( [TRACE_PARSING, [TRACE_SCANNING]] )
	   Parse one complete BLAST result and return it.  If no results on input stream, returns "undef".  In case of parser error it die()s with
	   an (at present not very useful) error message.

	   The following structure is returned in a hash reference:

	     {
	       blast_version =>    STRING,
	       references =>	   [ STRING, ... ],
	       rounds => [
		   {
		       oneline_idx =>	   NUM,    # index of first one-line description of
						   # round in "onelines"
		       oneline_cnt =>	   NUM,    # number of one-line descriptions of round
						   # in "onelines"
		       hit_idx =>	   NUM,    # index of first hit of round in "hits"
		       hit_cnt =>	   NUM,    # number of hits of round in "hits"
		       oneline_new_idx =>  NUM|undef# index of first new (not-seen-before)
						   # one-line description of round
		       oneline_new_cnt =>  NUM	   # number of new one-line descriptions of
						   # 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
	     }

	   If you want tracing for parsing and scanning, you can enable them using the parameters of this call.

       result()
	   Returns the last BLAST result parsed or "undef" if no last result.

       get_trace_scanning()
	   Returns scan trace state as a Boolean value.

       set_trace_scanning( BOOLEAN )
	   Set scan trace - debugging aid.

SEE ALSO

       Zerg(3pm), Zerg::Report(3pm)

AUTHOR

       Laszlo Kajan, <lkajan@rostlab.org>

COPYRIGHT AND LICENSE

       Copyright (C) 2012 by Laszlo Kajan

       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.

perl v5.14.2							    2012-03-29						    RG::Blast::Parser(3pm)