[Bioperl-l] Filehandle issue

Chris Fields cjfields at uiuc.edu
Tue Jan 16 13:04:00 EST 2007


All,

I have noticed an interesting problem when running tests on a bioperl  
bug (http://tinyurl.com/tamf8).  Several Bio::AlignIO parsers, such  
as Bio::AlignIO::phylip, return 0 instead of using 'return', which  
causes problems when using newFh() for retrieving an IO::Handle:

----------------------------

$in = Bio::AlignIO->newFh(-fh => \*STDIN,
                      -format => 'phylip');

# $in is a GLOB

while( my $aln = <$in>)
{
     print $aln->no_sequences(),"\n";
}

----------------------------

cjfields:~/tests/phylip cjfields$ more testaln.phylip | ./alignio.pl
4
Can't call method "no_sequences" without a package or object  
reference at ./alignio.pl line 28, <STDIN> line 10.

The method call works for the first loop iteration, but the while  
loop test evaluates '0' as true in this case.  I think it's b/c perl  
is treating the returned 0 like general text retrieved from a file  
handle (the string '0') instead of EOF (with would return undef).  I  
ran a quick check on this and 'return 0' is used quite a bit in other  
IO modules (though not all).  Changing the 'return 0' to a simple  
'return' fixes the problem.

How common is the above while loop idiom used when iterating through  
data via a file handle?

chris



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