[Bioperl-l] remoteblast
Brian Osborne
bosborne11 at verizon.net
Fri Mar 12 17:46:52 UTC 2010
Please google "svn update bioperl".
On Mar 12, 2010, at 12:36 PM, Roopa Raghuveer wrote:
> Hello all,
>
> I am trying remote blast program and connecting to NCBI Blast, but I am
> unable to retrieve the sequences. Chris had suggested me to update from SVN.
> Could you please tell me how to update it from SVN?
>
> Regards,
> Roopa.
>
> On Sun, Mar 7, 2010 at 6:48 PM, Roopa Raghuveer <rtbio.2009 at gmail.com>wrote:
>
>> Hi Chris,
>>
>> Thank you very much for the information. Could you please tell me how to
>> update it from SVN?
>>
>> Thanks and regards,
>> Roopa
>>
>>
>> On Sun, Mar 7, 2010 at 3:57 PM, Chris Fields <cjfields at illinois.edu>wrote:
>>
>>> Roopa,
>>>
>>> I committed a fix for this a few days ago; if you update from SVN it
>>> should work. The problem stemmed from server-side changes at NCBI.
>>>
>>> chris
>>>
>>> On Mar 7, 2010, at 7:11 AM, Roopa Raghuveer wrote:
>>>
>>>> Hello Mark and everybody,
>>>>
>>>> I have been trying to connect to remote blast to retrieve similar
>>> sequences
>>>> to a given sequence. But my program is unable to retrieve the sequences
>>> from
>>>> BLAST, i.e., it is getting executed till the remote blast ids, but it is
>>> not
>>>> entering the else loop after collecting the rid. Please check this
>>> problem
>>>> and help me in this regard. I think the problem is in getting the
>>> sequence
>>>> and going to the 'else' part. i.e.,
>>>>
>>>> else {
>>>>
>>>> open(OUTFILE,'>',$blastdebugfile); # I think the problem
>>> is
>>>> in else part, i.e., it is not taking the next result.#
>>>> print OUTFILE "else entered";
>>>> close(OUTFILE);
>>>>
>>>> my $result = $rc->next_result();
>>>>
>>>> #save the output
>>>>
>>>> Please give me your reply.
>>>>
>>>> Thanks and regards,
>>>> Roopa.
>>>>
>>>> My code is as follows.
>>>>
>>>> #!/usr/bin/perl
>>>>
>>>> #path for extra camel module
>>>> use lib "/srv/www/htdocs/rain/RNAi/";
>>>> use rnai_blast;
>>>>
>>>>
>>>> use Bio::SearchIO;
>>>> use Bio::Search::Result::BlastResult;
>>>> use Bio::Perl;
>>>> use Bio::Tools::Run::RemoteBlast;
>>>> use Bio::Seq;
>>>> use Bio::SeqIO;
>>>> use Bio::DB::GenBank;
>>>>
>>>> $serverpath = "/srv/www/htdocs/rain/RNAi";
>>>> $serverurl = "http://141.84.66.66/rain/RNAi";
>>>> $outfile = $serverpath."/rnairesult_".time().".html";
>>>> $nuc = $serverpath."/nuc".time().".txt";
>>>> $debugfile = $serverpath."/debug_".time().".txt";
>>>> $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
>>>>
>>>> my $outstring ="";
>>>>
>>>> &parse_form;
>>>>
>>>> print "Content-type: text/html\n\n";
>>>> print "<HTML>\n";
>>>> print "<head><title>RNAi Result</title>";
>>>> print "<META HTTP-EQUIV=\"Refresh\" CONTENT=\"30;
>>>> URL=$serverurl/rnairesult_".time().".html\"> \n";
>>>> print "</head>\n";
>>>> print "<body>\n";
>>>> print " Your results will appear <a
>>>> href=$serverurl/rnairesult_".time().".html>here</a><br>";
>>>> print " Please be patient, runtime can be up to 5 minutes<br>";
>>>> print " This page will automatically reload in 30 seconds.";
>>>> print "</BODY>\n";
>>>> print "</HTML>\n";
>>>>
>>>> defined(my $pid = fork) or die "Can't fork: $!";
>>>> exit if $pid;
>>>> open STDIN, '/dev/null' or die "Can't read /dev/null: $!";
>>>> open STDOUT, '>/dev/null' or die "Can't write to /dev/null: $!";
>>>> open STDERR, '>&STDOUT' or die "Can't dup stdout: $!";
>>>>
>>>>
>>>>
>>>> open(OUTFILE, '>',$outfile);
>>>>
>>>> print OUTFILE "<HTML>\n
>>>> <head><title>RNAi Result</title>
>>>> <META HTTP-EQUIV=\"Refresh\" CONTENT=\"30;
>>>> URL=$serverurl//rnairesult_".time().".html\"> \n
>>>> <meta http-equiv=\"expires\" content=\"0\">
>>>> </head>\n
>>>> <body>\n
>>>> Your results will appear <a
>>>> href=$serverurl/rnairesult_".time().".html>here</a><br>
>>>> Please be patient, runtime can be up to 5 minutes <br>
>>>> This page will automatically reload in 30 seconds <br>
>>>> </BODY>\n
>>>> </HTML>\n";
>>>>
>>>> close(OUTFILE);
>>>>
>>>> @compseqs = blastcode($in{'Inputseq'},$in{'Organism'});
>>>>
>>>> $in{'Inputseq'} =~ s/>.*$//m;
>>>> $in{'Inputseq'} =~ s/[^TAGC]//gim;
>>>> $in{'Inputseq'} =~ tr/actg/ACTG/;
>>>>
>>>> @out = similar($in{'Inputseq'}, \@compseqs, $in{'Windowsize'},
>>>> $in{'Threshold'});
>>>>
>>>>
>>>> sub blastcode
>>>> {
>>>>
>>>> $inpu1= $_[0];
>>>>
>>>> $organ= $_[1];
>>>>
>>>> open(NUC,'>',$nuc);
>>>> print NUC $inpu1,"\n";
>>>> close(NUC);
>>>>
>>>> my $prog = 'blastn';
>>>> my $db = 'refseq_rna';
>>>> my $e_val= '1e-10';
>>>> my $organism= $organ;
>>>>
>>>> $gb = new Bio::DB::GenBank;
>>>>
>>>> my @params = ( '-prog' => $prog,
>>>> '-data' => $db,
>>>> '-expect' => $e_val,
>>>> '-readmethod' => 'SearchIO',
>>>> '-Organism' => $organism );
>>>>
>>>> open(OUTFILE,'>',$blastdebugfile);
>>>> print OUTFILE @params;
>>>> close(OUTFILE);
>>>>
>>>>
>>>> my $factory = Bio::Tools::Run::RemoteBlast->new(@params, -ENTREZ_QUERY
>>> =>
>>>> "$organ\[ORGN]");
>>>>
>>>> #my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>>>>
>>>> #change a paramter
>>>>
>>>> #$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Trypanosoma
>>>> Brucei[ORGN]';
>>>>
>>>> #change a paramter
>>>> # $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} =
>>> '$input2[ORGN]';
>>>>
>>>> my $v = 1;
>>>> #$v is just to turn on and off the messages
>>>>
>>>> my $str = Bio::SeqIO->new('-file' => $nuc , '-format' => 'fasta' ,
>>>> '-organism' => "$organ\[ORGN]");
>>>>
>>>> while (my $input = $str->next_seq())
>>>> {
>>>> #Blast a sequence against a database:
>>>> #Alternatively, you could pass in a file with many
>>>> #sequences rather than loop through sequence one at a time
>>>> #Remove the loop starting 'while (my $input = $str->next_seq())'
>>>> #and swap the two lines below for an example of that.
>>>> open(OUTFILE,'>',$debugfile);
>>>> print OUTFILE $input;
>>>> close(OUTFILE);
>>>>
>>>> #submits the input data to BLAST#
>>>>
>>>> my $r = $factory->submit_blast($input);
>>>>
>>>> open(OUTFILE,'>',$debugfile);
>>>> print OUTFILE $r;
>>>> close(OUTFILE);
>>>>
>>>>
>>>> print STDERR "waiting...." if($v>0);
>>>>
>>>> while ( my @rids = $factory->each_rid ) {
>>>> open(OUTFILE,'>',$debugfile);
>>>> # print OUTFILE "while entered";
>>>> close(OUTFILE);
>>>> foreach my $rid ( @rids ) {
>>>>
>>>> open(OUTFILE,'>',$debugfile);
>>>> # print OUTFILE "foreach entered";
>>>> close(OUTFILE);
>>>> #Retrieving the result ids#
>>>>
>>>> my $rc = $factory->retrieve_blast($rid);
>>>>
>>>> if( !ref($rc) )
>>>> {
>>>> if( $rc < 0 )
>>>> {
>>>> $factory->remove_rid($rid);
>>>> }
>>>> open(OUTFILE,'>',$debugfile);
>>>> # print OUTFILE "if entered";
>>>> close(OUTFILE);
>>>> print STDERR "." if ( $v > 0 );
>>>> sleep 5;
>>>> }
>>>>
>>>> else {
>>>>
>>>> open(OUTFILE,'>',$blastdebugfile); # I think the problem
>>> is
>>>> in else part, i.e., it is not taking the next result.#
>>>> print OUTFILE "else entered";
>>>> close(OUTFILE);
>>>>
>>>> my $result = $rc->next_result();
>>>>
>>>> #save the output
>>>> $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
>>>>
>>>> open(BLASTDEBUGFILE,'>',$blastdebugfile);
>>>> print BLASTDEBUGFILE $result->next_hit();
>>>> close(BLASTDEBUGFILE);
>>>> #saving the output in blastdata.time.out file#
>>>>
>>>> # $random=rand();
>>>>
>>>> my $filename = $serverpath."/blastdata_".time()."\.out";
>>>> # open(DEBUGFILE,'>',$debugfile);
>>>> # open(new,'>',$filename);
>>>> # @arra=<new>;
>>>> # print DEBUGFILE @arra;
>>>> # close(DEBUGFILE);
>>>> # close(new);
>>>>
>>>> $factory->save_output($filename);
>>>>
>>>> # open(BLASTDEBUGFILE,'>',$debugfile);
>>>> # print BLASTDEBUGFILE "Hello $rid";
>>>> # close(BLASTDEBUGFILE);
>>>>
>>>> $factory->remove_rid($rid);
>>>>
>>>> open(BLASTDEBUGFILE,'>',$blastdebugfile);
>>>> # print BLASTDEBUGFILE $organism;
>>>> close(BLASTDEBUGFILE);
>>>>
>>>> # open(OUTFILE,'>',$outfile);
>>>> # print OUTFILE "Test2 $result->database_name()";
>>>> # close(OUTFILE);
>>>>
>>>> #$hit = $result->next_hit;
>>>> #open(new,'>',$debugfile);
>>>> #print $hit;
>>>> #close(new);
>>>> $dummy=0;
>>>> while ( my $hit = $result->next_hit ) {
>>>>
>>>> next unless ( $v >= 0);
>>>>
>>>> # open(OUTFILE,'>',$debugfile);
>>>> # print OUTFILE "$hit in while hits";
>>>> # close(OUTFILE);
>>>>
>>>> my $sequ = $gb->get_Seq_by_version($hit->name);
>>>> my $dna = $sequ->seq(); # get the sequence as a string
>>>> $dummy++;
>>>> open(OUTFILE,'>',$debugfile);
>>>> # print OUTFILE $dna;
>>>> close(OUTFILE);
>>>> push(@seqs,$dna);
>>>> }
>>>> }
>>>> }
>>>> }
>>>> }
>>>>
>>>> $warum=@seqs;
>>>> open(OUTFILE,'>',$debugfile);
>>>> # print OUTFILE $warum;
>>>> print OUTFILE @seqs;
>>>> close(OUTFILE);
>>>>
>>>>
>>>> return(@seqs); #returning the sequences obtained on BLAST#
>>>> }
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
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