[Bioperl-l] bug report - SeqIO::genbank.pm

[Brian Osborne]

Qunfeng,

In the future please submit bugs at http://bugzilla.bioperl.org/.

Right now I'll just take a look at this without a formal bug report, thanks
for the submission.

Brian O.


On 8/26/05 3:26 PM, "Qunfeng" <qfdong at iastate.edu> wrote:

> Hi there,
> 
> Sorry I am not sure where to report bioperl bug and whether this bug has
> been reported before. So I am just going to send it to the bioperl list.
> 
> The "_read_GenBank_Species" function in SeqID::genbank.pm generates an
> exception when parsing GenBank record GI#66271013, which has an unusual
> ORGANISM name "(Populus tomentosa x P. bolleana) x P. tomentosa var.
> truncata". Notice there is a "(" in the beginning.  That "(" will be
> treated as an opening "(" for regular expression (see line 8 below) and can
> be fixed by a simple escaping (see line 7 below).
> 
> 
> =================================================
> sub _read_GenBank_Species{                              ...
>    elsif (/^\s{2}ORGANISM/o) {
>       my @spflds = split(' ', $_);
>        ($ns_name) = $_ =~ /\w+\s+(.*)/o;
>        shift(@spflds); # ORGANISM
>        $spflds[0] =~
> s/\(/\\\(/;                                          #(7)  escape the ( by \(
>        if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) {  #(8)  it
> causes exception with "(Populus"
>            $organelle = shift(@spflds);
>        }
>        ...
> }
> =================================================
> 
> Qunfeng
> 
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