I have the fallowing code(see below) and it is giving me this error 

Use of /c modifier is meaningless without /g at hwk5.pl line 31. Barew
+ord found where operator expected at hwk5.pl line 31, near "-database
+ => '/class"
  (Might be a runaway multi-line // string starting on line 4)(Missing
+ operator before lass?)
Unquoted string "lass" may clash with future reserved word at hwk5.pl 
+line 31.
syntax error at hwk5.pl line 31, near "-database=> '/class"
Execution of hwk5.pl aborted due to compilation errors.

[download]

Here is the code and I will mark line 31 by ******** 

use Bio::SeqIO;
use Bio::SearchIO;
use Bio::Tools::Run::StandAloneBlast;
use strict

print "Write the file name from where you are getting the sequence
form\n\n";
$file=<STDIN>;
chomp $file;

print "Write put the name of the output file\n\n";
$output=<STDIN>;
chomp $output;

#declare the required object
my $seqio= '';
my $seqobj= '';
my $factory = '';
my $blast_report= '';
my $out_file= '';

$seqio= Bio::SeqIO->new(-file => $file,
                        -format=> 'fasta');

while ($seqobj = $seqio->next_seq()) {
$factory = Bio::Tools::Run::StandAloneBlast->new(
-program =>'blastn',
***************-database => '/class/bi617a/share/blast/data/rat.rna.fn
+a',
-e=> 1e-6,
_READMETHOD=> "Blast" );
$out_file = $seqobj->display_id . $outfile;
$factory->outfile($out_file);
$blast_report = $factory->blastall($seqobj); }

#the blast output name
my $filename= $outfile;

#create an object tot he blast output file
my $input= Bio::SearchIO->(-format => 'blastn',
                           -file   => $filename);
#Print out the query, hit names and percent indenty, percent query ali
+gned
 print
"QueryName\tQueryLenght\tLengthMatch\tAccesionNumber\tDescription\tRan
+k\tScore\%ID\tStartPostQ\tEndPosQ\tStartPosH\tEndPosH\n";

#Go thru the BLAST reports one by one

while (my $result = $report->next_result)
{
    while($hit=$result->next_hit)
        {#Go through eadch HSP for this sequence
        while ($hsp= $hit->next_hsp)
    {
        #Print some tab-delimited data about this HSP
        print $result->query_name, "\t";
        print $result->query_length, "\t";
        print $hsp->hsp_length, "\t";
        print $result->query_accession, "\t";
        print $hit->description, "\t";
        print $hsp->rank, "\t";
        print $hsp->score, "\t";
        print $hsp->percent_identity, "\t";
        print $hsp->start('query'), "\t";
        print $hsp->end('query'), "\t";
        print $hsp->start('hit'), "\t";
        print $hsp->end('hit'), "\t";
        }
        }
}

[download]

In reply to Bioperl FASTA parsing by rolandomantilla

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