[Bioperl-l] about bioperl issue
Hsueh
lovebaby39 at gmail.com
Thu Dec 10 15:53:00 UTC 2009
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
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