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  1. JohnLucania

    Output generation with loop on the fly

    I opt to use the existing modules rather than reinventing wheels. print "writing results"; our $filename; while ( my @rids = $fac->each_rid ) { die "No record found\n" unless @rids; foreach my $rid ( @rids ) { my $result = $fac->retrieve_blast( $rid ); if( ref( $result )) {...
  2. JohnLucania

    Output generation with loop on the fly

    I see. Can you introduce the option 1)? [ponder]
  3. JohnLucania

    Output generation with loop on the fly

    with #use strict; I am getting the one big file still. So, I guess use strict; shouldn't be an issue here. [ponder]
  4. JohnLucania

    Output generation with loop on the fly

    Yes, I have it. #! /usr/bin/perl -w use strict; use warnings; $|++; use Bio::Perl; use Bio::Tools::Run::RemoteBlast; use Bio::Search::Result::ResultI; use Bio::Search::Hit::HitI; use Bio::Search::HSP::HSPI; use Bio::DB::RandomAccessI; use Bio::DB::Query::GenBank; use Bio::DB::GenBank; use...
  5. JohnLucania

    Output generation with loop on the fly

    It still generate one big file only. any ideas? [ponder]
  6. JohnLucania

    Output generation with loop on the fly

    ok, $fac is: my $fac = Bio::Tools::Run::RemoteBlast->new( -prog => 'blastp', -data => 'nr' , -expect => $evalue , -readmethod => 'SearchIO' ); my $gb_dbh = Bio::DB::GenBank->new(-format => 'fasta'); my $str = $gb_dbh->get_Seq_by_acc( $accession ); print...
  7. JohnLucania

    Output generation with loop on the fly

    while ( my @rids = $fac->each_rid ) { die "No record found\n" unless @rids; foreach my $rid ( @rids ) { my $result = $fac->retrieve_blast( $rid ); if( ref( $result )) { my $output = $result->next_result(); my $filename = $output->query_name().".out"; $filename...
  8. JohnLucania

    pod format

    What is the recommened/common pod format/template in practice? Of course, they will vary, but in general? I have an example: =pod =head1 NAME Debugging mod_perl Perl Internals =head1 Description This document explains how to debug Perl code under mod_perl. =head1 Maintainers Maintainer...
  9. JohnLucania

    Can't modify constant item in scalar assignment

    I got it. Thanks a bunch! jl
  10. JohnLucania

    Can't modify constant item in scalar assignment

    What is this error about and how to fix? Can't modify constant item in scalar assignment at line 16, near "}" #! /usr/bin/perl use strict; use warnings; package Protein; our %attrib; sub new { my( $class , %attribs ) = ( @_ ); my $obj = { _name =...
  11. JohnLucania

    Inserting data

    How do you parse the data (Seq.txt) into a table in mysql? The txt data look like: >AREDD7|Mus musculus|brain|45545|411|741 aagcggccggtctgcagtcggagacttgcaggcagcaaacacggtgcgaacgaaccggag gggggagagagaaatcaaacagctaagcgtggagcagacggcctgggacccagaagggga tcgatgcgaggagcgcaataata...
  12. JohnLucania

    passing to query

    ok, I got it working. :-) jl
  13. JohnLucania

    passing to query

    You are right. They are wrapped.. #!/usr/local/bin/perl use CGI::Carp qw/fatalsToBrowser/; use CGI; use strict; use DBI; my $q=new CGI; my $obj = new CGI; my $name = 'Search Seq'; my $title = 'Search Seq'; print $obj->header ( 'text/html' ); $obj->start_html ( $title ); $obj->h1 (...
  14. JohnLucania

    passing to query

    This is what I have: #!/usr/local/bin/perl use CGI; use strict; use DBI; my $q=new CGI; my $obj = new CGI; my $name = 'Search mRNA'; my $title = 'Search mRNA'; print $obj->header ( 'text/html' ); $obj->start_html ( $title ); $obj->h1 ( {-class=>'header'}, $title ); my...
  15. JohnLucania

    passing to query

    bla... $qe->finish; $dc->disconnect (); // I am trying to populate the form right below the result display so that you can run the query right on the page w/o going back to the previous page. // ./SearchSeqResult.cgi >/dev/null retruns no error, but no form shows up on the result...
  16. JohnLucania

    passing to query

    Chris, This takes care of the issue. Thanks a bunch.. jl
  17. JohnLucania

    passing to query

    I removed these extra: my $method = 'post'; my $action = 'SearchSeqResult.cgi';
  18. JohnLucania

    passing to query

    Thank for the tip. This give no errors, but no result (blank page) shows up on the result cgi page. Why is that? #!/usr/local/bin/perl use CGI; use strict; use DBI; my $q=new CGI; my $obj = new CGI; my $name = 'Search mRNA'; my $method = 'post'; my $action = 'SearchSeqResult.cgi'; my...
  19. JohnLucania

    passing to query

    KevinADC, yes, that part works well. Thanks a bunch!! jl
  20. JohnLucania

    passing to query

    ./SearchSeqResult.cgi > /dev/null returns no error, but when I run the cgi pages, I get: Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Why is that? Thanks, jl

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