[Bioperl-l] Bio::ASN1::EntrezGene now on Github

[Carnë Draug]

On 10 September 2013 17:47, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Sep 10, 2013, at 11:20 AM, Carnë Draug <carandraug+dev at gmail.com> wrote:
>
>> On 9 Sep 2013 16:41:50, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
>>> All,
>>>
>>> I contacted Mingyi Liu, the author of Bio::ASN1::EntrezGene, about putting his code up on Github and he enthusiastically agreed.  Based on his feedback I have added it (from his latest CPAN release) as a git repository here (under the bioperl account):
>>>
>>>    https://github.com/bioperl/Bio-ASN1-EntrezGene
>>>
>>> I'll work on migrating any outstanding issue to Github as well.
>>>
>>> chris
>>
>> Hi
>>
>> I have contacted him some time ago about a bug fix which I believe was
>> never released. At the time there was no public repository of the
>> package so I just created one [1] for him to see the patch [2].
>>
>> In addition, to that, there are two other ``bugs'' reported [1] with
>> fixes. One is just a matter of setting the correct permisions for the
>> files, and the other is a spelling mistake on the documentation.
>> Finally, his email address needs an update since it no longer works.
>> His current email address is <mingyiliu at gmail.com>
>>
>> Carnë
>>
>> [1] https://github.com/carandraug/bio-asn1-entrezgene
>> [2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b
>> [3] https://rt.cpan.org/Public/Dist/Display.html?Name=Bio-ASN1-EntrezGene
>
> …and so you can now, with the magic of github, make the changes directly to the repo

Yeah. But what I wanted was to discuss the implications of that
change. It is related to a previous discussion [1]. If memory serves
me right, this patch would read the whole sequences of a set rather
than one at a time. I have used this module directly, not through the
bioperl module, so I'm unsure if it will break things there.

There's also the thing that next_seq() was always returning an array
reference with only 1 element (the one sequence). Now there will be
more elements (one per sequence in the Entrezgene set). People
expecting the old behaviour will be skipping data unless maybe some
warning is printed or some other change is performed. Specially
next_seq returning many sequences (the next set) is misleading.

Finally, there's also the thing that the patch reads an entire set
which for all we know, can be thousands of sequences.

Carnë

[1] http://bioperl.996286.n3.nabble.com/sets-of-sequences-how-to-read-td16940.html