From georgkam at gmail.com  Mon Dec  8 01:49:23 2008
From: georgkam at gmail.com (George Githinji)
Date: Mon, 8 Dec 2008 09:49:23 +0300
Subject: [BioRuby] bio::blast::reports
Message-ID: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>

Hi all
Using bio 1.2.1 with ruby 1.8.6 on ubuntu 8.01 the following code seems not
to print anything.
just wondering why.

require 'rubygems'
require 'bio'

report_file = "/home/george/esther_blast_files/blast_output2.txt"
Bio::Blast.reports(report_file) do |report|
  puts report.class
  puts "am going away"
end

report_file is a valid blast report file in m0 format.

-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/

From ngoto at gen-info.osaka-u.ac.jp  Mon Dec  8 02:51:49 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 8 Dec 2008 16:51:49 +0900
Subject: [BioRuby] bio::blast::reports
In-Reply-To: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>
References: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>
Message-ID: <20081208075150.131DA1CBC443@idnmail.gen-info.osaka-u.ac.jp>

On Mon, 8 Dec 2008 09:49:23 +0300
"George Githinji" <georgkam at gmail.com> wrote:

> Hi all
> Using bio 1.2.1 with ruby 1.8.6 on ubuntu 8.01 the following code seems not
> to print anything.
> just wondering why.
> 
> require 'rubygems'
> require 'bio'
> 
> report_file = "/home/george/esther_blast_files/blast_output2.txt"
> Bio::Blast.reports(report_file) do |report|
>   puts report.class
>   puts "am going away"
> end
> 
> report_file is a valid blast report file in m0 format.

Please see document of Bio::Blast.reports.
http://bioruby.rubyforge.org/classes/Bio/Blast.html#M000732
It says "only for xml format".

For default (-m 0) format, Bio::FlatFile.open(filename)
can be used.


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

From ktym at hgc.jp  Mon Dec  8 18:07:00 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Tue, 9 Dec 2008 08:07:00 +0900
Subject: [BioRuby] bio::blast::reports
In-Reply-To: <20081208075150.131DA1CBC443@idnmail.gen-info.osaka-u.ac.jp>
References: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>
	<20081208075150.131DA1CBC443@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <65E67872-3D8C-480B-8414-9991ABF07D5B@hgc.jp>

Goto-san,

Is it impossible to make Bio::Blast.reports understand -m 0 format?

Toshiaki

On 2008/12/08, at 16:51, Naohisa GOTO wrote:

> On Mon, 8 Dec 2008 09:49:23 +0300
> "George Githinji" <georgkam at gmail.com> wrote:
>
>> Hi all
>> Using bio 1.2.1 with ruby 1.8.6 on ubuntu 8.01 the following code seems not
>> to print anything.
>> just wondering why.
>>
>> require 'rubygems'
>> require 'bio'
>>
>> report_file = "/home/george/esther_blast_files/blast_output2.txt"
>> Bio::Blast.reports(report_file) do |report|
>>  puts report.class
>>  puts "am going away"
>> end
>>
>> report_file is a valid blast report file in m0 format.
>
> Please see document of Bio::Blast.reports.
> http://bioruby.rubyforge.org/classes/Bio/Blast.html#M000732
> It says "only for xml format".
>
> For default (-m 0) format, Bio::FlatFile.open(filename)
> can be used.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From andrew.j.grimm at gmail.com  Mon Dec  8 19:27:32 2008
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Tue, 9 Dec 2008 11:27:32 +1100
Subject: [BioRuby] bl2seq question
Message-ID: <b9140daa0812081627p5b8c54f7td7f8f49f8b536d96@mail.gmail.com>

If you want to compare two sequences using bl2seq, is it possible to get
Bioruby to execute the comparison, or do you need to do that part yourself
(using files written to disk and system calls) and then create a
Bio::Blast::Bl2seq::Report object from the resulting file's contents?

Thanks,

Andrew Grimm

From tomoakin at kenroku.kanazawa-u.ac.jp  Mon Dec  8 23:56:29 2008
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Tue, 9 Dec 2008 13:56:29 +0900
Subject: [BioRuby] bl2seq question
In-Reply-To: <b9140daa0812081627p5b8c54f7td7f8f49f8b536d96@mail.gmail.com>
References: <b9140daa0812081627p5b8c54f7td7f8f49f8b536d96@mail.gmail.com>
Message-ID: <91CAE1C5-71B2-40B5-A8BD-6354196A977A@kenroku.kanazawa-u.ac.jp>

Hi,

Surely, it is possible to make ruby execute the command.
I originally wrote Bl2seq as such.
To pass the two sequences without writing to temporary files,
I used a trick to use three forks and /dev/fd/
which will not be very portable.
Thus, I think it is too tricky to incorporate into a general ruby  
library like bioruby,
and have sent only the result formatting code.
A more portable way is to write the two sequences to temporary files and
then call bl2seq, delete the two files afterwards.

Sending the data to some http server might be written in a portable way,
though I didn't like idea to pay overheads to send to
a http server just for comparing two sequences.
(I didn't try and thus have no measurement for the performance)

-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan


From georgkam at gmail.com  Tue Dec  9 08:32:07 2008
From: georgkam at gmail.com (George Githinji)
Date: Tue, 9 Dec 2008 16:32:07 +0300
Subject: [BioRuby] bio::blast::reports
Message-ID: <55915f820812090532m660ef5a5xb3f84aa417ae5eae@mail.gmail.com>

Hi Naohisa,
Thank you for the reply. I also think that making bio::blast::reports
understand m0 format would be a good idea since it is the default blast
output and the one most molecular biologists are likely to want to parse.


-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/

From ngoto at gen-info.osaka-u.ac.jp  Tue Dec 30 06:49:41 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 30 Dec 2008 20:49:41 +0900
Subject: [BioRuby] bio::blast::reports
In-Reply-To: <55915f820812090532m660ef5a5xb3f84aa417ae5eae@mail.gmail.com>
References: <55915f820812090532m660ef5a5xb3f84aa417ae5eae@mail.gmail.com>
Message-ID: <20081230114944.329B51CBC413@idnmail.gen-info.osaka-u.ac.jp>

Hi, 

I've changed the Bio::Blast.reports to support default (-m 0)
and tabular (-m 8) formats in addition to XML format.
It will be included in the next release.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Tue, 9 Dec 2008 16:32:07 +0300
"George Githinji" <georgkam at gmail.com> wrote:

> Hi Naohisa,
> Thank you for the reply. I also think that making bio::blast::reports
> understand m0 format would be a good idea since it is the default blast
> output and the one most molecular biologists are likely to want to parse.
> 
> 
> -- 
> ---------------
> Sincerely
> George
> 
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From georgkam at gmail.com  Mon Dec  8 06:49:23 2008
From: georgkam at gmail.com (George Githinji)
Date: Mon, 8 Dec 2008 09:49:23 +0300
Subject: [BioRuby] bio::blast::reports
Message-ID: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>

Hi all
Using bio 1.2.1 with ruby 1.8.6 on ubuntu 8.01 the following code seems not
to print anything.
just wondering why.

require 'rubygems'
require 'bio'

report_file = "/home/george/esther_blast_files/blast_output2.txt"
Bio::Blast.reports(report_file) do |report|
  puts report.class
  puts "am going away"
end

report_file is a valid blast report file in m0 format.

-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/


From ngoto at gen-info.osaka-u.ac.jp  Mon Dec  8 07:51:49 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 8 Dec 2008 16:51:49 +0900
Subject: [BioRuby] bio::blast::reports
In-Reply-To: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>
References: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>
Message-ID: <20081208075150.131DA1CBC443@idnmail.gen-info.osaka-u.ac.jp>

On Mon, 8 Dec 2008 09:49:23 +0300
"George Githinji" <georgkam at gmail.com> wrote:

> Hi all
> Using bio 1.2.1 with ruby 1.8.6 on ubuntu 8.01 the following code seems not
> to print anything.
> just wondering why.
> 
> require 'rubygems'
> require 'bio'
> 
> report_file = "/home/george/esther_blast_files/blast_output2.txt"
> Bio::Blast.reports(report_file) do |report|
>   puts report.class
>   puts "am going away"
> end
> 
> report_file is a valid blast report file in m0 format.

Please see document of Bio::Blast.reports.
http://bioruby.rubyforge.org/classes/Bio/Blast.html#M000732
It says "only for xml format".

For default (-m 0) format, Bio::FlatFile.open(filename)
can be used.


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


From ktym at hgc.jp  Mon Dec  8 23:07:00 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Tue, 9 Dec 2008 08:07:00 +0900
Subject: [BioRuby] bio::blast::reports
In-Reply-To: <20081208075150.131DA1CBC443@idnmail.gen-info.osaka-u.ac.jp>
References: <55915f820812072249r504f11d4kc7af567043f68b02@mail.gmail.com>
	<20081208075150.131DA1CBC443@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <65E67872-3D8C-480B-8414-9991ABF07D5B@hgc.jp>

Goto-san,

Is it impossible to make Bio::Blast.reports understand -m 0 format?

Toshiaki

On 2008/12/08, at 16:51, Naohisa GOTO wrote:

> On Mon, 8 Dec 2008 09:49:23 +0300
> "George Githinji" <georgkam at gmail.com> wrote:
>
>> Hi all
>> Using bio 1.2.1 with ruby 1.8.6 on ubuntu 8.01 the following code seems not
>> to print anything.
>> just wondering why.
>>
>> require 'rubygems'
>> require 'bio'
>>
>> report_file = "/home/george/esther_blast_files/blast_output2.txt"
>> Bio::Blast.reports(report_file) do |report|
>>  puts report.class
>>  puts "am going away"
>> end
>>
>> report_file is a valid blast report file in m0 format.
>
> Please see document of Bio::Blast.reports.
> http://bioruby.rubyforge.org/classes/Bio/Blast.html#M000732
> It says "only for xml format".
>
> For default (-m 0) format, Bio::FlatFile.open(filename)
> can be used.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From andrew.j.grimm at gmail.com  Tue Dec  9 00:27:32 2008
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Tue, 9 Dec 2008 11:27:32 +1100
Subject: [BioRuby] bl2seq question
Message-ID: <b9140daa0812081627p5b8c54f7td7f8f49f8b536d96@mail.gmail.com>

If you want to compare two sequences using bl2seq, is it possible to get
Bioruby to execute the comparison, or do you need to do that part yourself
(using files written to disk and system calls) and then create a
Bio::Blast::Bl2seq::Report object from the resulting file's contents?

Thanks,

Andrew Grimm


From tomoakin at kenroku.kanazawa-u.ac.jp  Tue Dec  9 04:56:29 2008
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Tue, 9 Dec 2008 13:56:29 +0900
Subject: [BioRuby] bl2seq question
In-Reply-To: <b9140daa0812081627p5b8c54f7td7f8f49f8b536d96@mail.gmail.com>
References: <b9140daa0812081627p5b8c54f7td7f8f49f8b536d96@mail.gmail.com>
Message-ID: <91CAE1C5-71B2-40B5-A8BD-6354196A977A@kenroku.kanazawa-u.ac.jp>

Hi,

Surely, it is possible to make ruby execute the command.
I originally wrote Bl2seq as such.
To pass the two sequences without writing to temporary files,
I used a trick to use three forks and /dev/fd/
which will not be very portable.
Thus, I think it is too tricky to incorporate into a general ruby  
library like bioruby,
and have sent only the result formatting code.
A more portable way is to write the two sequences to temporary files and
then call bl2seq, delete the two files afterwards.

Sending the data to some http server might be written in a portable way,
though I didn't like idea to pay overheads to send to
a http server just for comparing two sequences.
(I didn't try and thus have no measurement for the performance)

-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan



From georgkam at gmail.com  Tue Dec  9 13:32:07 2008
From: georgkam at gmail.com (George Githinji)
Date: Tue, 9 Dec 2008 16:32:07 +0300
Subject: [BioRuby] bio::blast::reports
Message-ID: <55915f820812090532m660ef5a5xb3f84aa417ae5eae@mail.gmail.com>

Hi Naohisa,
Thank you for the reply. I also think that making bio::blast::reports
understand m0 format would be a good idea since it is the default blast
output and the one most molecular biologists are likely to want to parse.


-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/


From ngoto at gen-info.osaka-u.ac.jp  Tue Dec 30 11:49:41 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 30 Dec 2008 20:49:41 +0900
Subject: [BioRuby] bio::blast::reports
In-Reply-To: <55915f820812090532m660ef5a5xb3f84aa417ae5eae@mail.gmail.com>
References: <55915f820812090532m660ef5a5xb3f84aa417ae5eae@mail.gmail.com>
Message-ID: <20081230114944.329B51CBC413@idnmail.gen-info.osaka-u.ac.jp>

Hi, 

I've changed the Bio::Blast.reports to support default (-m 0)
and tabular (-m 8) formats in addition to XML format.
It will be included in the next release.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Tue, 9 Dec 2008 16:32:07 +0300
"George Githinji" <georgkam at gmail.com> wrote:

> Hi Naohisa,
> Thank you for the reply. I also think that making bio::blast::reports
> understand m0 format would be a good idea since it is the default blast
> output and the one most molecular biologists are likely to want to parse.
> 
> 
> -- 
> ---------------
> Sincerely
> George
> 
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby