[BioRuby] samtools-ruby
Raoul Bonnal
bonnalraoul at ingm.it
Fri Feb 4 13:57:07 UTC 2011
In these days, w.e. too, I have no time for sam tools. From the next week I could spend more time on this project and improve test, usability and platform supports.
On 04/feb/2011, at 14.13, Michal wrote:
> Hi,
> I would be happy if would find out how to get on a particular position the alignment and then I could give feedback.
>
> Pysam http://code.google.com/p/pysam/ contains all files and tests.
> ~/Downloads/pysam-0.3.1/tests$ ls
> 00README.txt ex4.sam ex8.sam Makefile
> ex1.fa ex5.sam example.gtf.gz pysam_test.py
> ex1.sam.gz ex6.sam example.gtf.gz.tbi segfault_tests.py
> ex3.sam ex7.sam example.py tabix_test.py
>
> Maybe it would be possible to test bioruby-samtools in the same way. Pysam is ship out with samtools source code and maybe could be used it for bioruby-samtools.
>
> Thank you in advance.
>
> Michal
>
>
> On 02/04/2011 10:26 PM, Tomoaki NISHIYAMA wrote:
>>
>> Hi,
>>
>>> What I have forgotten to do?
>>
>> Now, you are at the point I reached yesterday and
>> I don't think you have forgotten anything.
>>
>> From yesterday's mail:
>>> 1) Failure:
>>> test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]:
>>> hey buddy, you should probably rename this file and start testing for real
>>>
>>> Loading seems ok.
>>> I'm not sure if this is bad or ok.
>>
>> You could look at test/test_bio-samtools.rb
>> $ cat test/test_bio-samtools.rb
>> require 'helper'
>>
>> class TestBioSamtools < Test::Unit::TestCase
>> should "probably rename this file and start testing for real" do
>> flunk "hey buddy, you should probably rename this file and start testing for real"
>> end
>> end
>>
>> and guess what it means.
>>
>> My guess is that this is test not implemented yet.
>> So, this error does not tell if the library function well or can not used at all.
>> You might just try what you wanted to do and see if it works.
>>
>>> I understand how difficult it is to keep track and it is a good idea to ship bioruby-samtools
>>> with a working samtools version like Raoul does it.
>>
>>
>> My view is the opposite.
>> Since it potentially has many bugs and changes rapidly, bundled shipping is ineffective.
>> With the lack of test code, we cannot even tell which is a good working version.
>> --
>> Tomoaki NISHIYAMA
>>
>> Advanced Science Research Center,
>> Kanazawa University,
>> 13-1 Takara-machi,
>> Kanazawa, 920-0934, Japan
>>
>
--
R.J.P.B.
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