[Bioperl-l] bioperl 1.4 SearchIO doesn't work parsing Blast output

Wed Feb 8 23:34:45 UTC 2006

Hubert,

Give me a bit to look over your code and think this through. I am still
re-familiarizing myself with the relevant modules, so I can't give an answer
off the top of my head.

Also, please send me one or more of your blast reports (zipped) if you don't
mind (and maybe avoid including the list in your reply). Let's take this
"offline" relative to the list - we'll include the list again if there is a
Bioperl issue and solution. (In case you are concerned at all, I promise not
to share or study the actual BLAST results.)

I'm not particularly familiar with the Fedora distributions, but I'm sure I
can either chase down the perl problem or at least eliminate everything else
but Fedora as the culprit. ;}

(Chris - I'm not quite paying attention on an hourly basis yet, but I do
intend to help support these issues for the foreseeable future. Thanks as
always for the assist.)

Thanks!

Roger Hall
Technical Director
MidSouth Bioinformatics Center
University of Arkansas at Little Rock
(501) 569-8074

-----Original Message-----
From: Hubert Prielinger [mailto:hubert.prielinger at gmx.at] 
Sent: Wednesday, February 08, 2006 4:23 PM
To: Chris Fields; bioperl-l at bioperl.org; rahall2 at ualr.edu
Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work parsing Blast
output

hi,
I have installed from the following page: 
http://news.open-bio.org/archives/2005_10.html,  the Core, Run and Ext. 
I'm using only the SearchIO without remoteblast module, because I have 
already all my Blast output files.
My operating system is fedora core 9.

Code:

#!/usr/bin/perl -w

use Bio::SearchIO;

print "start program\n";
my $directory = 
"/home/Hubert/installed/eclipse/workspace/Database_Search/result_4";
opendir(DIR, $directory) || die("Cannot open directory");
print "opened directory\n";

foreach my $file (readdir(DIR))  {
print "read file\n";

my $search = new Bio::SearchIO (-format => 'blast',
                                -file => $file);

my $cutoff_len = 10;

#iterate over each query sequence
while (my $result = $search->next_result) {
print "entered 1st while loop\n";

    #iterate over each hit on the query sequence
    while (my $hit = $result->next_hit) {

        #iterate over each HSP in the hit
        while (my $hsp = $hit->next_hsp) {

            if ($hsp->length('sbjct') <= $cutoff_len) {
                #print $hsp->hit_string, "\n";
                for ($hsp->hit_string) {

                    if (tr/K// >= 2 || tr/R// >= 2 && tr/W// >= 2 || 
tr/K// == 1 && tr/R// == 1 && tr/W// >= 2) {

                        # Print some tab-delimited data about this HSP

                           open (bigShot, ">>BlastOutputTrial.txt") || 
die ("Could not open file. $!");
                                #print $result->query_name, "\t";

#                        print $hit->significance, "\t";
                         print bigShot $hit->name, "-->";
                         print bigShot $hit->description, "\n";
                         #print bigShot "Query:   ", 
$hsp->start('query'), "  ", $hsp->query_string, "  ", 
$hsp->end('query'), "\n";
                         print bigShot "Seq:     ", $hsp->start('hit'), 
"  ", $hsp->hit_string, "  ", $hsp->end('hit'), "\n";

#                        print $hsp->rank, "\t";
#                        print $hsp->percent_identity, "\t";
#                        print $hsp->evalue, "\t";
#                        print $hsp->hsp_length, "\n";

                        close (bigShot);

                    };

            }
        }
        }
    }
}

}

closedir(DIR);

Chris Fields wrote:

>Make sure you ran a full installation of bioperl-1.5.1 or bioperl-live (not
>just the modules you want; mixing bioperl versions might work, but you
might
>run into interoperability problems).  Then replace the Bio::SearchIO::blast
>with the one in Bugzilla.  The 'other option' you mentioned might be trying
>XML instead of text, which is more stable in the long run.  You will still
>need to run a full upgrade to bioperl 1.5.1 for that; make sure you read
>this:
>
>http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast
>
>If you're using SearchIO directly instead of Remoteblast, you should be
able
>to set the '-readmethod' flag to 'blastxml'.
>
>It also wouldn't hurt to know what OS you're using or see some code.  Roger
>is out there somewhere (I think) and may also have some input.
>
>Christopher Fields
>Postdoctoral Researcher - Switzer Lab
>Dept. of Biochemistry
>University of Illinois Urbana-Champaign  
>
>  
>
>>-----Original Message-----
>>From: Hubert Prielinger [mailto:hubert.prielinger at gmx.at] 
>>Sent: Wednesday, February 08, 2006 3:41 PM
>>To: Chris Fields; bioperl-l at bioperl.org
>>Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
>>parsing Blast output
>>
>>hi chris,
>>thanks, I have upgraded to version 1.5.1 but it isn't still 
>>working, do you have any ohter idea, the problem I have is 
>>that I have to parse a lot of textfiles....
>>or shall I look for another option to parse those files...
>>
>>regards
>>Hubert
>>
>>
>>
>>Chris Fields wrote:
>>
>>    
>>
>>>My guess is you're running into text parsing problems in 
>>>Bio::SearchIO::blast.  Upgrade to the latest developer 
>>>      
>>>
>>version (1.5.1) 
>>    
>>
>>>or bioperl-live (CVS), then see the bug below.
>>>
>>>http://bugzilla.bioperl.org/show_bug.cgi?id=1934
>>>
>>>I think the first problem you ran into is solved in bioperl 
>>>      
>>>
>>1.5.1, the 
>>    
>>
>>>last problem (more recent, not related to the first) has 
>>>      
>>>
>>been fixed but 
>>    
>>
>>>hasn't been committed to bioperl-live yet.  The fixed 
>>>      
>>>
>>SearchIO::blast 
>>    
>>
>>>is available in the link above, but realize it hasn't been 
>>>      
>>>
>>committed yet and may change.
>>    
>>
>>>Christopher Fields
>>>Postdoctoral Researcher - Switzer Lab
>>>Dept. of Biochemistry
>>>University of Illinois Urbana-Champaign
>>>
>>> 
>>>
>>>      
>>>
>>>>-----Original Message-----
>>>>From: bioperl-l-bounces at lists.open-bio.org
>>>>[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hubert 
>>>>Prielinger
>>>>Sent: Wednesday, February 08, 2006 2:52 PM
>>>>To: bioperl-l at bioperl.org
>>>>Subject: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
>>>>        
>>>>
>>parsing Blast 
>>    
>>
>>>>output
>>>>
>>>>Hi,
>>>>If I want to parse a Blast Output (Version 2.2.12) with 
>>>>        
>>>>
>>Bio::SearchIO, 
>>    
>>
>>>>I get the following error message:
>>>>
>>>>MSG: no data for midline Query  1   WWWKWRW  7
>>>>STACK Bio::SearchIO::blast::next_result
>>>>/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
>>>>STACK toplevel
>>>>/home/Hubert/installed/eclipse/workspace/Database_Search/Blast.pl:21
>>>>
>>>>is that a bug......
>>>>
>>>>If I want to parse Blast Output (version 2.2.13), I don't get 
>>>>anything.....
>>>>I'm using bioperl 1.4
>>>>
>>>>before, I have installed bioperl 1.4, it worked fine parsing Blast 
>>>>Output (version 2.2.12), but I don't remember which bioperl 
>>>>        
>>>>
>>version I 
>>    
>>
>>>>had installed
>>>>
>>>>thanks in advance
>>>>
>>>>Hubert
>>>>
>>>>
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at lists.open-bio.org
>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>   
>>>>
>>>>        
>>>>
>>> 
>>>
>>>      
>>>
>
>
>  
>