[Bioperl-l] SearchIO newbie question

[Melodee Patterson]

Thank you to those who responded (so quickly!) to my dilemma. Apparently 
Bio::SearchIO::Writer::TextResultWriter is as close as I can get to the 
original report. Unfortunately, it changes the report enough that my other 
scripts will need to be extensively reworked in order to use them. But, the 
module has given me some great ideas on how I can rewrite those existing 
reports. (If  I can convince my boss that change is not always bad!)

Thanks again.

Melodee

----- Original Message ----- 
From: "Andrew Walsh" <walsh at cenix-bioscience.com>
To: "Melodee Patterson" <mpatterson at lucigen.com>
Cc: <bioperl-l at portal.open-bio.org>
Sent: Tuesday, May 24, 2005 10:07 AM
Subject: Re: [Bioperl-l] SearchIO newbie question


> Hello Melodee,
>
> I think what you want to do is to use one of the Bio::SearchIO::Writer::* 
> modules.
>
> This is a link to the HowTo describing how to use these:
>
> http://bioperl.org/HOWTOs/SearchIO/outputting.html
>
>
> Basically, you want to create a Bio::SearchIO::Writer::TextResultWriter 
> object and use this to set the 'writer' attribute in the constructor for 
> Bio::SearchIO.
>
> Here is an example:
>
> my $writer = new Bio::SearchIO::Writer::TextResultWriter();
> my $out = new Bio::SearchIO(-writer => $writer,
>               -file   => ">your_file.txt");
>
> while ( my $blast = $in->next_result() )
>     $out->write_result($blast);
> }
>
> That should do the trick.
>
> Andrew
>
> Melodee Patterson wrote:
>> Hello,
>>
>> I have written a number of perl and bioperl scripts to parse large phage 
>> BLASTx files, and now my boss wants me to remove some bacterial 
>> contaminations before I run my reports. I know how to use Bio::SearchIO 
>> to bring in the blast reports, and I know how to find the reports that I 
>> don't want using regular expressions, but what I can't figure out is how 
>> to write the good BLAST reports out to a file just as they are. I don't 
>> want to parse them at all, since my other scripts are expecting them as 
>> full BLAST reports and I'd rather not rewrite them.
>>
>> If I can do this:
>>
>> use Bio::SeqIO;
>> $in = Bio::SeqIO->new('-file' => "AIZX_test.fas",
>>                       '-format' => 'Fasta');
>> $out = Bio::SeqIO->new('-file' => ">AIZX_test_out.txt",
>>                       '-format' => 'Fasta');
>> while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }
>>
>>
>> why can't I do this:
>>
>> use Bio::SearchIO;
>> $in = Bio::SearchIO->new('-file' => "BLASTx_test.txt",
>>                       '-format' => 'blast');
>> $out = Bio::SearchIO->new('-file' => ">BLASTx_test_out.txt",
>>                        '-format' => 'blast');
>> while ( my $blast = $in->next_result() ) {$out->write_result($blast); }
>>
>> Thanks - I appreciate any help I can get!
>>
>> Melodee
>> Lucigen Corp.
>> 608-831-9011
>> mpatterson at lucigen.com
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> -- 
> ------------------------------------------------------------------
> Andrew Walsh, M.Sc.
> Bioinformatics Software Engineer
> IT Unit
> Cenix BioScience GmbH
> Tatzberg 47
> 01307 Dresden
> Germany
> Tel. +49-351-4173 137
> Fax  +49-351-4173 109
>
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> ------------------------------------------------------------------
>
>