Hello all i would like to blast multiple sequence individually one after another and output i need in excel sheet, i tried like this:
use Bio::Tools::Run::StandAloneBlastPlus; Bio.SearchIO.BlastIO.blast_xml use Excel::Writer::XLSX; use strict; use Bio::SearchIO; for file in *.fasta do echo $file out=`echo $file | sed 's/_.fasta_/_.excel_/'` my $factory = Bio::Tools::Run::StandAloneBlastPlus->new( -db_data => 'Autotransporters.fasta', # Specifies the file to use for database -create => 1 # Creates a new temporary database ); my $result = $factory->blastn( -query => '$file', # Specifies the query file -outfile => '$out' ); # Specifies the output location $factory->cleanup; # Deletes the temporary database files
Error :
"use" not allowed in expression at multifasta_blast.pl line 3, at end of line syntax error at multifasta_blast.pl line 3, near "blast_xml use Excel::Writer::XLSX" BEGIN not safe after errors--compilation aborted at multifasta_blast.pl line 4.
Can anyone help me out to solve the error .