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)

Bio::SearchIO::hmmer_pull(3pm)				User Contributed Perl Documentation			    Bio::SearchIO::hmmer_pull(3pm)

NAME

       Bio::SearchIO::hmmer_pull - A parser for HMMER output

SYNOPSIS

	   # do not use this class directly it is available through Bio::SearchIO
	   use Bio::SearchIO;
	   my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
				      -file   => 't/data/hmmpfam.bigout');
	   while (my $result = $in->next_result) {
	       # this is a Bio::Search::Result::HmmpfamResult object
	       print $result->query_name(), " for HMM ", $result->hmm_name(), "
";
	       while (my $hit = $result->next_hit) {
		   print $hit->name(), "
";
		   while (my $hsp = $hit->next_hsp) {
		       print "length is ", $hsp->length(), "
";
		   }
	       }
	   }

DESCRIPTION

       This object implements a pull-parser for HMMER output. It is fast since it only does work on request (hence 'pull').

FEEDBACK

   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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::SearchIO::hmmer_pull->new();
	Function: Builds a new Bio::SearchIO::hmmer_pull object
	Returns : Bio::SearchIO::hmmer_pull
	Args	: -fh/-file => HMMER output filename
		  -format   => 'hmmer_pull'
		  -evalue   => float or scientific notation number to be used
			       as an evalue cutoff for hits
		  -score    => integer or scientific notation number to be used
			       as a score value cutoff for hits
		  -hsps     => integer minimum number of hsps (domains) a hit must have
		  -piped_behaviour => 'temp_file'|'memory'|'sequential_read'

		  -piped_behaviour defines what the parser should do if the input is
		   an unseekable filehandle (eg. piped input), see
		   Bio::PullParserI::chunk for details. Default is 'sequential_read'.

   next_result
	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

   result_count
	Title	: result_count
	Usage	: my $count = $searchio->result_count
	Function: Returns the number of results we have processed.
	Returns : integer
	Args	: none

   rewind
	Title	: rewind
	Usage	: $searchio->rewind;
	Function: Allow one to reset the Result iterator to the beginning, so that
		  next_result() will subsequently return the first result and so on.

		  NB: result objects are not cached, so you will get new result objects
		  each time you rewind. Also, note that result_count() counts the
		  number of times you have called next_result(), so will not be able
		  tell you how many results there were in the file if you use rewind().

	Returns : n/a
	Args	: none

perl v5.14.2							    2012-03-02					    Bio::SearchIO::hmmer_pull(3pm)