blast_parse_1.pl

#!/usr/local/bin/perl -w

# Parsing BLAST reports with BioPerl's Bio::Tools::BPlite module
# WI Biocomputing course - Unix and Programming Skills for Biologists - March 2003

# See documentation at http://www.bioperl.org/Core/POD/Bio/Tools/BPlite.html

use Bio::Tools::BPlite;

# Prompt the user for the file name if it's not an argument
# NOTE: BLAST file must be in text (not html) format
if (! $ARGV[0])
{
   print "What is the BLAST file to parse? ";

   # Get input and remove the newline character at the end
   chomp ($inFile = <STDIN>);
}
else
{
   $inFile = $ARGV[0];
}

$report = new Bio::Tools::BPlite(-file=>"$inFile");

# Count hits
$i = 1;

print "HIT_NUM\tSCORE\tBITS\tPERCENT\tEXPECT\tSUBJECT_NAME\tIDENTITIES\tMATCH_LENGTH\t";
print "QUERY_START\tQUERY_END\tSUBJECT_START\tSUBJECT_END\n";
print "\n**** DATA FOR QUERY ", $report->query, "****\n\n";

while(my $sbjct = $report->nextSbjct)
{
   while (my $hsp = $sbjct->nextHSP)
   {
      print "$i\t";
      print $hsp->score, "\t",
      $hsp->bits,   "\t",
      $hsp->percent, "\t",
      $hsp->P, "\t",
      $hsp->subject->seqname, "\t",
      $hsp->match, "\t",
      $hsp->length, "\t";
      # $hsp->querySeq,   "\t",     
      # $hsp->sbjctSeq,   "\t",     
      # $hsp->homologySeq, "\t",     
      print $hsp->query->start, "\t",
      $hsp->query->end, "\t",
      $hsp->subject->start, "\t",
      $hsp->subject->end, "\n";
   }
   $i++;
}