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.\" ========================================================================
.\"
.IX Title "Report 3pm"
.TH Report 3pm "2016-06-23" "perl v5.24.1" "User Contributed Perl Documentation"
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.SH "NAME"
Zerg::Report \- get attributes from a BLAST file in a data structure
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  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}\en";
\&      }
\&    }
\&  }
\&
\&  $zerg_report\->closeFile();
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 4
\&  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 = {
\&          \*(Aqquery_name\*(Aq => \*(AqME1\-0081T\-R227\-B12\-U.G\*(Aq,
\&          \*(Aqblast_version\*(Aq => \*(AqBLASTX 1.3.6 [2002\-03\-05]\*(Aq,
\&          \*(Aqbyte_offset\*(Aq => 4981,
\&          \*(Aqquery_length\*(Aq => \*(Aq444\*(Aq,
\&          \*(Aqquery_annotation\*(Aq => \*(Aq\*(Aq
\&          \*(Aqround_begins\*(Aq => [ 0, 129, 201 ], # indicates the first hit in each round of iterated blast
\&          \*(Aqhits\*(Aq => [
\&                      {
\&                        \*(Aqsubject_annotation\*(Aq => \*(Aq(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD\-e]\*(Aq,
\&                        \*(Aqhsps\*(Aq => [
\&                                    {
\&                                      \*(Aqquery_end\*(Aq => \*(Aq82\*(Aq,
\&                                      \*(Aqsubject_ali\*(Aq => \*(AqASELEIFAALIECEA\-GSTDYDGMLAVASVVMNRVNHRYYPDTITGVIYQSGQFSPVASGKLDKVLKRGIKSSCLEVAKDA\*(Aq,
\&                                      \*(Aqquery_ali\*(Aq => \*(AqDAQTRKLAAIAYGEASGANDANEIGGIAWAVANRARAWGGK\-TVDGLLAADPNYTYAVKDG\-NQRYAKLMKATEAAIAADP\*(Aq,
\&                                      \*(Aqsubject_end\*(Aq => \*(Aq328\*(Aq,
\&                                      \*(Aqidentities\*(Aq => \*(Aq15\*(Aq,
\&                                      \*(Aqscore\*(Aq => \*(Aq87\*(Aq,
\&                                      \*(Aqpercent_positives\*(Aq => \*(Aq41\*(Aq,
\&                                      \*(Aqgaps\*(Aq => \*(Aq3\*(Aq,
\&                                      \*(Aqscore_bits\*(Aq => \*(Aq37.9\*(Aq,
\&                                      \*(Aqalignment_length\*(Aq => \*(Aq81\*(Aq,
\&                                      \*(Aqevalue\*(Aq => \*(Aq0.40\*(Aq,
\&                                      \*(Aqpercent_identities\*(Aq => \*(Aq18\*(Aq,
\&                                      \*(Aqpositives\*(Aq => \*(Aq34\*(Aq,
\&                                      \*(Aqquery_start\*(Aq => \*(Aq4\*(Aq,
\&                                      \*(Aqsubject_start\*(Aq => \*(Aq249\*(Aq
\&                                    }
\&                                  ],
\&                        \*(Aqsubject_length\*(Aq => \*(Aq880\*(Aq,
\&                        \*(Aqsubject_name\*(Aq => \*(Aqgi|16802882|ref|NP_464367.1|\*(Aq
\&                      },
\&                    ],
\&        };
.Ve
.SH "AUTHORS"
.IX Header "AUTHORS"
Apu� Paquola <apua@iq.usp.br>, Abimael Machado <abimael@iq.usp.br> IQ-USP Bioinformatics Lab
.PP
Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Zerg