[Bioperl-l] EUtilities Cookbook example fails

Chris Fields cjfields at illinois.edu
Wed Jun 10 09:33:51 EDT 2009


Adam,

Okay, fixed that and the previous issue with 'use an undefined value  
as an ARRAY reference'.  The previous issue appears to be due to a  
change in the XML output from NCBI (it used to give the IDs at one  
point).  Also made the wiki changes for this; didn't take long to find  
everything.

Thanks for pointing that out!  If you find any more issues feel free  
to make the necessary changes on the wiki or point them out if they're  
in code.

chris

On Jun 10, 2009, at 8:12 AM, Adam Witney wrote:

> Hi Chris,
>
> not sure if I should start a new thread for this, but it is related  
> to the EUtilities Cookbook and LinkSet.pm.
>
> There are several references in the Cookbook to the method  
> "get_linkname", however this seems to have changed in the recent  
> version of LinkSet.pm to "get_link_name". But one reference to the  
> old method name still exists in LinkSet.pm, as shown by this patch:
>
> --- /usr/local/lib/perl5/site_perl/5.8.9/Bio/Tools/EUtilities/Link/ 
> LinkSet.pm	2009-02-20 12:36:37.000000000 +0000
> +++ /Users/adam/Desktop/LinkSet.pm	2009-06-10 13:58:49.000000000 +0100
> @@ -220,7 +220,7 @@
> =cut
>
> sub get_link_name {
> -    return ($_[0]->get_linknames)[0];
> +    return ($_[0]->get_link_names)[0];
> }
>
> =head2 get_submitted_ids
>
> If i haven't got this all wrong entirely, I could go through and fix  
> the Cookbook entries if that was useful?
>
> adam
>
>
> On 10 Jun 2009, at 13:28, Chris Fields wrote:
>
>> I can reproduce that; I'll look into it.
>>
>> chris
>>
>> On Jun 10, 2009, at 6:19 AM, Adam Witney wrote:
>>
>>> Hi,
>>>
>>> I am going through the EUtilities Cookbook, but the last example  
>>> (in section 2.3.1) fails with:
>>>
>>> Can't use an undefined value as an ARRAY reference at /usr/lib/ 
>>> perl5/site_perl/5.8.8/Bio/Tools/EUtilities/Link/LinkSet.pm line 470.
>>>
>>> This is with BioPerl 1.6.0, perl v5.8.8
>>>
>>> thanks for any help
>>>
>>> adam
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



More information about the Bioperl-l mailing list