[Bioperl-l] cdd-search with remoteblast?
Jonas Schaer
Brotelzwieb at gmx.de
Fri Jul 10 05:18:12 EDT 2009
Hi,
I tried to do what Malcom proposed my ($prog = 'rpsblast'; my $db =
'CDD';) but that didn't work.
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Value rpsblast for PUT parameter PROGRAM does not match expression
t?blast[
pnx]. Rejecting.
STACK: Error::throw
STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359
STACK: Bio::Tools::Run::RemoteBlast::submit_parameter
C:/Perl/site/lib/Bio/Tools
/Run/RemoteBlast.pm:329
STACK: Bio::Tools::Run::RemoteBlast::new
C:/Perl/site/lib/Bio/Tools/Run/RemoteBl
ast.pm:257
STACK: blast_a_seq2.pm:14
-----------------------------------------------------------
So I should try to "change the wrapper to allow 'rpsblast'", right? Could
You tell me how to do that, please? So sorry but I have no idea yet...:)
If that doesn't work, is there any other way to run cdd-searches with perl?
Thank you so much!
Regards, Jonas
----- Original Message -----
From: "Chris Fields" <cjfields1 at gmail.com>
To: "Cook, Malcolm" <MEC at stowers.org>
Cc: "'Jonas Schaer'" <Brotelzwieb at gmx.de>; "'BioPerl List'"
<bioperl-l at lists.open-bio.org>; "'Smithies, Russell'"
<Russell.Smithies at agresearch.co.nz>; <cjfields at bioperl.org>
Sent: Thursday, July 09, 2009 9:19 PM
Subject: Re: [Bioperl-l] cdd-search with remoteblast?
> I've scheduled this tentatively for the 1.6 release series (just not
> sure when yet). It may work as is, but I haven't tried it out yet
> (and am hazarding to guess it only retrieves the single main RID at
> the moment).
>
> chris
>
> On Jul 9, 2009, at 10:56 AM, Cook, Malcolm wrote:
>
>> Jonas,
>>
>> If you want to continue to use the bioperl remoteblast interface,
>> probably what you should do is simply call it twice.
>>
>> Once, as you already know how to do, which will return without CDD
>> results.
>>
>> Secondly, to get the CDD results, call remoteblast a second time.
>> This time, using
>> -database => 'CDD'
>> -program => 'rpsblast'
>>
>> However, the wrapper may object to the 'rpsblast' program. It is
>> not listed in the POD -
>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/Tools/Run/RemoteBlast.pm)
>> If so, my guess is that changing the perl wrapper to allow
>> rpsblast will "just work" (tm). I've cc:ed cjfields at bioperl.org for
>> his opinion on this.
>>
>> Also, you might want to perform the CDD search first, especially if
>> you are streaming results to eyeball that might like something to
>> look at while the second (presumably longer) search is running.
>>
>> Cheers,
>>
>> Malcolm Cook
>> Stowers Institute for Medical Research - Kansas City, Missouri
>>
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>> Jonas Schaer
>>> Sent: Thursday, July 09, 2009 5:16 AM
>>> To: BioPerl List; Smithies, Russell
>>> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
>>>
>>> Hi guys,
>>> Thank you all so much for your help and patience :). Of
>>> course you were right and I finaly found the right
>>> put-parameter to get exactly the same hits as on the homepage.
>>> I do have an other question though :)...
>>> I now want to include a search for conserved domains, but
>>> when I try to use the CDD_SEARCH-parameter
>>> (http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node16.html#
>>> sub:CDD_SEARCH)
>>> like the other put-parameters the way chris once told
>>> me(works fine with the other params):
>>>
>>> my %put = (
>>> WORD_SIZE => 3,
>>> HITLIST_SIZE => 100,
>>> THRESHOLD => 11,
>>> FILTER => 'R',
>>> GENETIC_CODE => 1,
>>> CDD_SEARCH => 'on'
>>> ###I tried it
>>> with 'true' and '1', too.
>>>
>>> );
>>>
>>> for my $putName (keys %put) {
>>> $factory->submit_parameter($putName,$put{$putName});
>>> }
>>>
>>>
>>> ...an exception is thrown:
>>>
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: CDD_SEARCH is not a valid PUT parameter.
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359
>>> STACK: Bio::Tools::Run::RemoteBlast::submit_parameter
>>> C:/Perl/site/lib/Bio/Tools
>>> /Run/RemoteBlast.pm:325
>>> STACK: main::blast_a_sequence firsteval0.8.pm:383
>>> STACK: main::blast_it firsteval0.8.pm:288
>>> STACK: firsteval0.8.pm:35
>>> ----------------------------------------------------------- .
>>> I guess somehow this could be the solution to my problem:
>>> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node78.html#s
>>> ub:RID-for-Simultaneous
>>> , but unfortunately I don't understand what to do.
>>> I'm so sorry to bother you with this but please help me once
>>> more...:)
>>>
>>> Best regards and thanks in advance,
>>> Jonas
>>>
>>> ----- Original Message -----
>>> From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
>>> To: "'Jonas Schaer'" <Brotelzwieb at gmx.de>
>>> Cc: "'Chris Fields'" <cjfields at illinois.edu>; "'BioPerl List'"
>>> <bioperl-l at lists.open-bio.org>
>>> Sent: Monday, July 06, 2009 10:56 PM
>>> Subject: RE: [Bioperl-l] different results with remote-blast skript
>>>
>>>
>>> Hi Jonas,
>>> You can't just play with the BLAST parameters and hope for a "better"
>>> result.
>>> I'd suggest that if you aren't sure what they do, you should
>>> leave them
>>> alone as small changes can make huge differences in the
>>> output - it's quite
>>> possible to miss finding what you're looking for by using the wrong
>>> parameters.
>>> If all else fails, read the blast manual:
>>> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall
>>> _all.html
>>> http://www.ncbi.nlm.nih.gov/blast/tutorial/
>>> Or Read Ian Korfs' excellent book:
>>> http://books.google.com/books?id=xvcnhDG9fNUC&lpg=PR17&ots=WJp
>> fuHF6Hn&dq=ian%20korf%20%20blast%20book&pg=PA3
>>>
>>> Don't worry about the integer overflow bug as there's nothing
>>> you can do
>>> about it. If you're interested, Google and Wikipedia are your
>>> friends:
>>> http://en.wikipedia.org/wiki/Integer_overflow
>>>
>>>
>>> Russell
>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>> bounces at lists.open-bio.org] On Behalf Of Jonas Schaer
>>>> Sent: Tuesday, 7 July 2009 12:14 a.m.
>>>> To: BioPerl List; Chris Fields
>>>> Subject: Re: [Bioperl-l] different results with remote-blast skript
>>>>
>>>> Hi guys, thanks for your answers so far.
>>>> @jason: integer overflow in blast.... sorry, but what do
>>> you mean by that?
>>>> how can I fix it...?
>>>>
>>>> Since I never really changed any parameters I thought them
>>> all to be
>>>> default.
>>>> whatever, I tried to get "better" results with my prog by changing
>>>> these:
>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
>>>>
>>> $Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATI
>>> STICS'} =
>>>> '1';
>>>> with no effect...I guess these were default values anyway.
>>>>
>>>> So please maybe you can tell me all the other parameters I
>>> can change with
>>>> my
>>>> perl-skript AND how to do that?
>>>> Unfortunately both, perl and the blast-algorithm are pretty
>>> much new to
>>>> me,
>>>> maybe thats why I just cannot find out how to do that on my
>>> own... :/
>>>>
>>>> Here is the output I get with my remote-blast skript:
>>>>
>>> ##############################################################
>>> ################
>>>> ###################################
>>>> Query Name:
>>>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLRSL
>>>> L
>>>> hit name is ref|XP_001702807.1|
>>>> score is 442
>>>> BLASTP 2.2.21+
>>>> Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro
>>> A. Schaffer,
>>>> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
>>> Lipman (1997),
>>>> "Gapped
>>>> BLAST and PSI-BLAST: a new generation of protein database search
>>>> programs",
>>>> Nucleic Acids Res. 25:3389-3402.
>>>>
>>>>
>>>> Reference for composition-based statistics: Alejandro A.
>>>> Schaffer, L. Aravind, Thomas L. Madden, Sergei Shavirin,
>>> John L. Spouge,
>>>> Yuri
>>>> I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
>>> "Improving the
>>>> accuracy of PSI-BLAST protein database searches with
>>> composition-based
>>>> statistics and other refinements", Nucleic Acids Res. 29:2994-3005.
>>>>
>>>>
>>>> RID: 53STX5G2013
>>>>
>>>>
>>>> Database: All non-redundant GenBank CDS
>>>> translations+PDB+SwissProt+PIR+PRF excluding environmental samples
>>>> from WGS projects
>>>> 9,252,587 sequences; 3,169,972,781 total letters Query=
>>>>
>>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLRSLL
>>>>
>>> DVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVARAWHERDDNAFRQAHQNTAM
>>>> ATGPDPDDEYE
>>>> Length=150
>>>>
>>>>
>>>>
>>> Score
>>>> E
>>>> Sequences producing significant alignments:
>>> (Bits)
>>>> Value
>>>>
>>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
>>> reinhard... 174
>>>> 2e-42
>>>>
>>>>
>>>> ALIGNMENTS
>>>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas reinhardtii]
>>>> gb|EDP06586.1| ClpS-like protein [Chlamydomonas reinhardtii]
>>>> Length=303
>>>>
>>>> Score = 174 bits (442), Expect = 2e-42, Method:
>>> Composition-based
>>>> stats.
>>>> Identities = 150/150 (100%), Positives = 150/150 (100%),
>>> Gaps = 0/150
>>>> (0%)
>>>>
>>>> Query 1
>>> MGSSSVGTYHLLLVLMgaggeqqavqagaevaSTEQVDGSGMAANSRGSTSGSEQPPrds
>>>> 60
>>>>
>>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDS
>>>> Sbjct 154
>>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDS
>>>> 213
>>>>
>>>> Query 61
>>> dlgllrslldVAGVDRTalevkllalaeagaeMPPAQDSQATAAGVVATLTSVYRQQVAR
>>>> 120
>>>>
>>> DLGLLRSLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVAR
>>>> Sbjct 214
>>> DLGLLRSLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVAR
>>>> 273
>>>>
>>>> Query 121 AWHERDDNAFRQAHQNTAMATGPDPDDEYE 150
>>>> AWHERDDNAFRQAHQNTAMATGPDPDDEYE
>>>> Sbjct 274 AWHERDDNAFRQAHQNTAMATGPDPDDEYE 303
>>>>
>>>>
>>>>
>>>> Database: All non-redundant GenBank CDS
>>>> translations+PDB+SwissProt+PIR+PRF
>>>> excluding environmental samples from WGS projects
>>>> Posted date: Jul 5, 2009 4:41 AM
>>>> Number of letters in database: -1,124,994,511
>>>> Number of sequences in database: 9,252,587
>>>>
>>>> Lambda K H
>>>> 0.309 0.122 0.345
>>>> Gapped
>>>> Lambda K H
>>>> 0.267 0.0410 0.140
>>>> Matrix: BLOSUM62
>>>> Gap Penalties: Existence: 11, Extension: 1
>>>> Number of Sequences: 9252587
>>>> Number of Hits to DB: 60273703
>>>> Number of extensions: 1448367
>>>> Number of successful extensions: 2103
>>>> Number of sequences better than 10: 0
>>>> Number of HSP's better than 10 without gapping: 0
>>>> Number of HSP's gapped: 2113
>>>> Number of HSP's successfully gapped: 0
>>>> Length of query: 150
>>>> Length of database: 3169972781
>>>> Length adjustment: 113
>>>> Effective length of query: 37
>>>> Effective length of database: 2124430450
>>>> Effective search space: 78603926650
>>>> Effective search space used: 78603926650
>>>> T: 11
>>>> A: 40
>>>> X1: 16 (7.1 bits)
>>>> X2: 38 (14.6 bits)
>>>> X3: 64 (24.7 bits)
>>>> S1: 42 (20.8 bits)
>>>> S2: 74 (33.1 bits)
>>>>
>>>>
>>> ##############################################################
>>> ################
>>>> ###################################
>>>> and here are the hits (?) of the blast-algorithm on the
>>> ncbi-homepage with
>>>> the same query of course:
>>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
>>> reinhard... 300
>>>> 3e-80
>>>> ref|XP_001942719.1| PREDICTED: similar to GA16705-PA
>>> [Acyrtho... 36.2
>>>> 1.1
>>>> ref|ZP_03781446.1| hypothetical protein RUMHYD_00880
>>> [Blautia... 35.4
>>>> 1.8
>>>> ref|XP_001563232.1| leucyl-tRNA synthetase [Leishmania
>>> brazil... 34.3
>>>> 4.2
>>>> ref|XP_680841.1| hypothetical protein AN7572.2
>>> [Aspergillus n... 33.5
>>>> 6.0
>>>> ref|YP_001768110.1| hypothetical protein M446_1150
>>> [Methyloba... 33.5
>>>> 7.0
>>>>
>>> ##############################################################
>>> ################
>>>> ###################################at
>>>> least the first hit is the same, but even there there is a
>>> different score
>>>> and e-value.
>>>>
>>>> thanks so much for any help :)
>>>> regards, jonas
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: "Chris Fields" <cjfields at illinois.edu>
>>>> To: "Jason Stajich" <jason at bioperl.org>
>>>> Cc: "Smithies, Russell"
>>> <Russell.Smithies at agresearch.co.nz>; "'BioPerl
>>>> List'" <bioperl-l at lists.open-bio.org>; "'Jonas Schaer'"
>>>> <Jonas_Schaer at gmx.de>
>>>> Sent: Monday, July 06, 2009 12:51 AM
>>>> Subject: Re: [Bioperl-l] different results with remote-blast skript
>>>>
>>>>
>>>>> That inspires confidence ;>
>>>>>
>>>>> chris
>>>>>
>>>>> On Jul 5, 2009, at 4:40 PM, Jason Stajich wrote:
>>>>>
>>>>>> integer overflow in blast....
>>>>>>
>>>>>> On Jul 5, 2009, at 2:00 PM, Smithies, Russell wrote:
>>>>>>
>>>>>>> I'd guess it's a difference in the parameters used.
>>>>>>> Interesting that both have the number of letters in the db as
>>>>>>> "-1,125,070,205", I assume that's a bug :-)
>>>>>>>
>>>>>>> Stats from your remote_blast:
>>>>>>>
>>>>>>> 'stats' => {
>>>>>>> 'S1' => '42',
>>>>>>> 'S1_bits' => '20.8',
>>>>>>> 'lambda' => '0.309',
>>>>>>> 'entropy' => '0.345',
>>>>>>> 'kappa_gapped' => '0.0410',
>>>>>>> 'T' => '11',
>>>>>>> 'kappa' => '0.122',
>>>>>>> 'X3_bits' => '24.7',
>>>>>>> 'X1' => '16',
>>>>>>> 'lambda_gapped' => '0.267',
>>>>>>> 'X2' => '38',
>>>>>>> 'S2' => '74',
>>>>>>> 'seqs_better_than_cutoff' => '0',
>>>>>>> 'posted_date' => 'Jul 4, 2009 4:41 AM',
>>>>>>> 'Hits_to_DB' => '60102303',
>>>>>>> 'dbletters' => '-1125070205',
>>>>>>> 'A' => '40',
>>>>>>> 'num_successful_extensions' => '2004',
>>>>>>> 'num_extensions' => '1436892',
>>>>>>> 'X1_bits' => '7.1',
>>>>>>> 'X3' => '64',
>>>>>>> 'entropy_gapped' => '0.140',
>>>>>>> 'dbentries' => '9252258',
>>>>>>> 'X2_bits' => '14.6',
>>>>>>> 'S2_bits' => '33.1'
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>> Stats from a blast done on the NCBI webpage:
>>>>>>>
>>>>>>> Database: All non-redundant GenBank CDS
>>> translations+PDB+SwissProt
>>>>>>> +PIR+PRF
>>>>>>> excluding environmental samples from WGS projects
>>>>>>> Posted date: Jul 4, 2009 4:41 AM
>>>>>>> Number of letters in database: -1,125,070,205
>>>>>>> Number of sequences in database: 9,252,258
>>>>>>>
>>>>>>> Lambda K H
>>>>>>> 0.309 0.124 0.340
>>>>>>> Gapped
>>>>>>> Lambda K H
>>>>>>> 0.267 0.0410 0.140
>>>>>>> Matrix: BLOSUM62
>>>>>>> Gap Penalties: Existence: 11, Extension: 1
>>>>>>> Number of Sequences: 9252258
>>>>>>> Number of Hits to DB: 86493230
>>>>>>> Number of extensions: 3101413
>>>>>>> Number of successful extensions: 9001
>>>>>>> Number of sequences better than 100: 65
>>>>>>> Number of HSP's better than 100 without gapping: 0
>>>>>>> Number of HSP's gapped: 9000
>>>>>>> Number of HSP's successfully gapped: 66
>>>>>>> Length of query: 150
>>>>>>> Length of database: 3169897087
>>>>>>> Length adjustment: 113
>>>>>>> Effective length of query: 37
>>>>>>> Effective length of database: 2124391933
>>>>>>> Effective search space: 78602501521
>>>>>>> Effective search space used: 78602501521
>>>>>>> T: 11
>>>>>>> A: 40
>>>>>>> X1: 16 (7.1 bits)
>>>>>>> X2: 38 (14.6 bits)
>>>>>>> X3: 64 (24.7 bits)
>>>>>>> S1: 42 (20.8 bits)
>>>>>>> S2: 65 (29.6 bits)
>>>>>>>
>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Jonas Schaer
>>>>>>>> Sent: Sunday, 28 June 2009 10:15 p.m.
>>>>>>>> To: BioPerl List
>>>>>>>> Subject: [Bioperl-l] different results with remote-blast skript
>>>>>>>>
>>>>>>>> Hi again :)
>>>>>>>> please, I only have this little question:
>>>>>>>> why do I get different results with my remote::blast
>>> perl skript
>>>>>>>> then on the
>>>>>>>> ncbi blast homepage?
>>>>>>>> I am using blastp, the query is an amino-sequence (different
>>>>>>>> results with any
>>>>>>>> sequence, differences not only in number of hits but even in e-
>>>>>>>> values, scores
>>>>>>>> etc...), the database is 'nr'.
>>>>>>>> PLEASE help me,
>>>>>>>> thank you in advance,
>>>>>>>> Jonas
>>>>>>>>
>>>>>>>> ps: my skript:
>>>>>>>>
>>>>
>>> ##############################################################
>>> ################
>>>>>>>> ##
>>>>>>>> use Bio::Seq::SeqFactory;
>>>>>>>> use Bio::Tools::Run::RemoteBlast;
>>>>>>>> use strict;
>>>>>>>> my @blast_report;
>>>>>>>> my $prog = 'blastp';
>>>>>>>> my $db = 'nr';
>>>>>>>> my $e_val= '1e-10';
>>>>>>>> #my $e_val= '10';
>>>>>>>> my @params = ( '-prog' => $prog,
>>>>>>>> '-data' => $db,
>>>>>>>> '-expect' => $e_val,
>>>>>>>> '-readmethod' => 'SearchIO' );
>>>>>>>> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
>>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
>>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
>>>>>>>> $
>>>>>>>> Bio
>>>>>>>>
>>> ::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'}
>>>>>>>> = '1';
>>>>>>>>
>>>>>>>> my
>>>>>>>> $
>>>>>>>> blast_seq
>>>>>>>>
>>> ='MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLR
>>>>>>>>
>>>>
>>> SLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVARAWHERDDN
>>> AFRQAHQNTAMATGPD
>>>>>>>> PDDEYE';
>>>>>>>> #$v is just to turn on and off the messages
>>>>>>>> my $v = 1;
>>>>>>>> my $seqbuilder = Bio::Seq::SeqFactory->new('-type' =>
>>>>>>>> 'Bio::PrimarySeq');
>>>>>>>> my $seq = $seqbuilder->create(-seq =>$blast_seq, -display_id =>
>>>>>>>> "$blast_seq");
>>>>>>>> my $filename='temp2.out';
>>>>>>>> my $r = $factory->submit_blast($seq);
>>>>>>>> print STDERR "waiting..." if( $v > 0 );
>>>>>>>> while ( my @rids = $factory->each_rid )
>>>>>>>> {
>>>>>>>> foreach my $rid ( @rids )
>>>>>>>> {
>>>>>>>> my $rc = $factory->retrieve_blast($rid);
>>>>>>>> if( !ref($rc) )
>>>>>>>> {
>>>>>>>> if( $rc < 0 )
>>>>>>>> {
>>>>>>>> $factory->remove_rid($rid);
>>>>>>>> }
>>>>>>>> print STDERR "." if ( $v > 0 );
>>>>>>>> }
>>>>>>>> else
>>>>>>>> {
>>>>>>>> my $result = $rc->next_result();
>>>>>>>> $factory->save_output($filename);
>>>>>>>> $factory->remove_rid($rid);
>>>>>>>> print "\nQuery Name: ",
>>> $result->query_name(),
>>>>>>>> "\n";
>>>>>>>> while ( my $hit = $result->next_hit )
>>>>>>>> {
>>>>>>>> next unless ( $v > 0);
>>>>>>>> print "\thit name is ", $hit->name, "\n";
>>>>>>>> while( my $hsp = $hit->next_hsp )
>>>>>>>> {
>>>>>>>> print "\t\tscore is ",
>>> $hsp->score, "\n";
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>>
>>>>>>>>
>>>>>>>> }
>>>>>>>> @blast_report = get_file_data ($filename);
>>>>>>>> return @blast_report;
>>>>>>>>
>>>>
>>> ##############################################################
>>> ################
>>>>>>>> ####
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>> =
>>>>>>> =
>>>>>>>
>>> =====================================================================
>>>>>>> Attention: The information contained in this message and/or
>>>>>>> attachments
>>>>>>> from AgResearch Limited is intended only for the
>>> persons or entities
>>>>>>> to which it is addressed and may contain confidential and/or
>>>>>>> privileged
>>>>>>> material. Any review, retransmission, dissemination or other use
>>>>>>> of, or
>>>>>>> taking of any action in reliance upon, this information
>>> by persons or
>>>>>>> entities other than the intended recipients is prohibited by
>>>>>>> AgResearch
>>>>>>> Limited. If you have received this message in error,
>>> please notify
>>>>>>> the
>>>>>>> sender immediately.
>>>>>>> =
>>>>>>> =
>>>>>>>
>>> =====================================================================
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> --
>>>>>> Jason Stajich
>>>>>> jason at bioperl.org
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>> --------------------------------------------------------------
>>> ----------------
>>>> --
>>>>
>>>>
>>>>
>>>> No virus found in this incoming message.
>>>> Checked by AVG - www.avg.com
>>>> Version: 8.5.375 / Virus Database: 270.13.5/2219 - Release
>>> Date: 07/05/09
>>>> 05:53:00
>>>
>>>
>>> --------------------------------------------------------------
>>> ------------------
>>>
>>>
>>>
>>> No virus found in this incoming message.
>>> Checked by AVG - www.avg.com
>>> Version: 8.5.375 / Virus Database: 270.13.5/2220 - Release
>>> Date: 07/05/09
>>> 17:54:00
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
--------------------------------------------------------------------------------
No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 8.5.375 / Virus Database: 270.13.8/2227 - Release Date: 07/09/09
05:55:00
More information about the Bioperl-l
mailing list