[Bioperl-l] how not to use Files when file handlers are required

[Guoneng Zhong]

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Hi,
I am starting to use Bioperl and I notice that often files are used as 
keepers of sequences and reports.  Either a file name is supplied as 
input or some file handler is required for input or output.  Case in 
point is the following example I copied from the tutorial:

use Bio::Tools::pSW;
   $factory = new Bio::Tools::pSW( '-matrix' => 'blosum62.bla',
                                   '-gap' => 12,
                                   '-ext' => 2, );
   $factory->align_and_show($seq1, $seq2, STDOUT);
   $aln = $factory->pairwise_alignment($seq1, $seq2);

My problem is that I don't work with files very much; I get my sequence 
either from someone's website or from a database.  So in the above 
example, how would I supply the matrix as a string if I don't have a 
file?  Do I have to write the string to a file first and then tell it?  
Same for the STDOUT; what if I want to use a String instead?  I come 
from a java background, and it has a String IO Stream reader/writer.  I 
wonder in Perl there is something like that or if Bioperl accommodates 
for this.

Thanks,
Guoneng

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Content-Transfer-Encoding: 7bit
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Hi,

I am starting to use Bioperl and I notice that often files are used as
keepers of sequences and reports.  Either a file name is supplied as
input or some file handler is required for input or output.  Case in
point is the following example I copied from the tutorial:


<fixed><fontfamily><param>Courier New</param>use Bio::Tools::pSW;

  $factory = new Bio::Tools::pSW( '-matrix' => 'blosum62.bla',

                                  '-gap' => 12,

                                  '-ext' => 2, );

  $factory->align_and_show($seq1, $seq2, STDOUT);

  $aln = $factory->pairwise_alignment($seq1, $seq2);</fontfamily></fixed>


My problem is that I don't work with files very much; I get my
sequence either from someone's website or from a database.  So in the
above example, how would I supply the matrix as a string if I don't
have a file?  Do I have to write the string to a file first and then
tell it?  Same for the STDOUT; what if I want to use a String instead? 
I come from a java background, and it has a String IO Stream
reader/writer.  I wonder in Perl there is something like that or if
Bioperl accommodates for this.


Thanks,

Guoneng
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