[BioRuby] samtools-ruby

[Raoul Bonnal]

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.