[Bioperl-l] Bug in the Bio::SeqIO.scf.pm code

Anthony Underwood Anthony.Underwood at hpa.org.uk
Mon Jan 29 06:29:16 EST 2007


Hi All,

 

Has anybody else come across this problem:

 

I have some scf files that fail to be read by the next_seq method within
scf.pm due to line 226: my $name_comment = $name_comments[0]->as_text();

Error: can not call method as_text on undefined object.

 

It appears that if the scf file has no comments then the array
@name_comments created in the previous line is empty.

 

I overcame this by replacing line 226 with the following lines:

my $name_comment;

if (@name_comments){

     $name_comment = $name_comments[0]->as_text();

     $name_comment =~ s/^Comment:\s+//;

}

 

 

Should this be incorporated into the code? Many thanks,

 

Anthony




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