[Bioperl-l] about bioperl issue

[Hsueh]

Dear Dave Messina

Thank you for your replies.

Reginald Hsueh

--------------------------------------------------
From: "Dave Messina" <David.Messina at sbc.su.se>
Sent: Thursday, December 10, 2009 11:36 PM
To: "Hsueh" <lovebaby39 at gmail.com>
Cc: <bioperl-l at bioperl.org>
Subject: Re: [Bioperl-l] about bioperl issue

> Hi Reginald,
>
> Please keep all replies on the list so that everyone can follow the 
> thread.
>
> In a separate email, Scott gave the answer you were looking for,  I think.
>
> Namely:
>   $hsp->query_string()
> OR
>   $hsp->hit_string()
>
>
>
> Dave
>
>
>
>
> On Dec 10, 2009, at 16:31, Hsueh wrote:
>
>> Dear Dave Messina
>>
>> I need to get the string that is 
>> "ctctttactcttaggtttacccgccggggtatcgtggcaaacaaggatagtttaaacaga".
>>
>> Thank you
>>
>> Reginald Hsueh
>>
>> ------------------------------------------------------------------------------------------------------------------------------
>> Query: 147 ctctttactcttaggtttacccgccggggtatcgtggcaaacaaggatagtttaaacaga 
>> 206
>>                  |||||| ||||||||||||||||||    |||| || |||||| 
>> |||||||||||| ||
>> Sbjct: 114   ctcttttctcttaggtttacccgccaatatatcctgtcaaacactgatagtttaaactga 
>> 173
>> ------------------------------------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>> --------------------------------------------------
>> From: "Dave Messina" <David.Messina at sbc.su.se>
>> Sent: Thursday, December 10, 2009 11:09 PM
>> To: "Hsueh" <lovebaby39 at gmail.com>
>> Cc: <bioperl-l at bioperl.org>
>> Subject: Re: [Bioperl-l] about bioperl issue
>>
>>> Hi Reginald,
>>>
>>> None of the words in your email or the attachment are colored red — 
>>> unfortunately any kind of formatting tends to get removed from emails 
>>> send to mailing lists.
>>>
>>> Could you be more specific about what part of the blast report you are 
>>> not able to get? You could even just copy and paste that particular bit 
>>> of the report into your reply if it's not clear what to call it.
>>>
>>>
>>> Dave




>>>>Dear
>>>>
>>>>The following is code.
>>>>
>>>>
>>>>--------------------------------------------------------------------------------
>>>>
>>>>my at params_rb = ( 'program'  => 'blastn',
>>>>            'database' => 'DB\\RB_GUS\\RB_GUS');
>>>>my $factory_rb = Bio::Tools::Run::StandAloneBlast->new(@params_rb);
>>>>
>>>>my $input_rb = Bio::Seq->new(-id  =>"test_query",
>>>>                       -seq => $testline2);
>>>>my $blast_report_rb = $factory_rb->blastall($input_rb);
>>>>
>>>> while (my $result_rb =  $blast_report_rb-> next_result ) {
>>>>  while (my $hit_rb = $result_rb->next_hit()){
>>>>   while (my $hsp_rb = $hit_rb->next_hsp()){
>>>>    print $hit_rb->name,"\nevalue = " ,  $hsp_rb->evalue , "\t score = " 
>>>> , $hsp_rb->score , "\n" ;
>>>>    #print " ",$hit->name,"\n";
>>>>   }
>>>>  }
>>>> }
>>>>
>>>>--------------------------------------------------------------------------------
>>>>
>>>>
>>>>I know how to get "name", "evalue" and  "score", but I don't know how 
>>>>to get the word which is in red color. (or please see attachment.)
>>>>------------------------------------------------------------------------------------------------------------------
>>>>Query: 147 ctctttactcttaggtttacccgccggggtatcgtggcaaacaaggatagtttaaacaga 
>>>>206
>>>>                   |||||| ||||||||||||||||||    |||| || |||||| 
>>>> |||||||||||| ||
>>>>Sbjct: 114 
>>>>ctcttttctcttaggtttacccgccaatatatcctgtcaaacactgatagtttaaactga 173
>>>>------------------------------------------------------------------------------------------------------------------
>>>>
>>>>I will appreciate if you could tell me how to do it.
>>>>Thank you.
>>>>
>>>>Reginald Hsueh