[Bioperl-l] chance database from swissprot to fasta

[James Wasmuth]

Hi Hafiz,

it's a mistake I still make ;o)

my $seq_out = Bio::SeqIO->new(-file=>
">$outFile",'-format'=> "$format1");


Note the '>' before $outfile

-james


hafiz hafiz wrote:

>Please some one can help me, i want to chance my
>database from swissprot to fasta but it can’t write to
>output file and i don’t know the bioperl modul can
>read my database file,
>
>This my code  
>
>#! usr\bin\perl
>
>use Bio::Root::IO;
>use Bio::SeqIO;
>use Bio::Seq;
>use Bio::Seq::RichSeq;
>use Location;  
>
>
>$format = swiss;
>$format1 = fasta;
>#Load  module Location.pm into an array
>@filelocation = Location::filelocation ("sprot42.dat",
>$database);
>
>  
>#Access directory path that resides in second element
>of array @filelocation
> my $location = $filelocation[1];
>
> 
>chdir $location;
>        print "$location\n";
>  
>#Open the directory that are returned by Location.pm
>modul
> opendir (DIR, $location)|| die "\nCouldn't open
>directory or directory not found\n";
>
>   
>#Read the drectory and store its content in an array
>  @file = readdir (DIR);
>   
> foreach $file(@file) {
>
> 
>  if ($file eq "sprot42.dat") {
>  
>print "\nEnter filename for output file:";
>chomp ($outFile = <STDIN>);
>        
>
>  
>my $seq_in = Bio::SeqIO->new(-file=>$file,'-format'=>
>"$format");
>   
>my $seq_out = Bio::SeqIO->new(-file=>
>"$outFile",'-format'=> "$format1");
>
>my $inseq;
>          while ( $inseq = $seq_in->next_seq) {
>             $seq_out->write_seq($inseq);
>          }
>        
>}
>}
>--------------------------------------------------------------------------------------------------------
>my output
>
>Enter filename for output
>file:/home/database/Bioperl/outFILE.pl
>
>
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