Report_HTML_DB/README.pod
=pod
if (defined($config->{"blast_dir"})){
$blast_dir = $config->{"blast_dir"};
}
=cut
=head2 getPipeline
Title : getPipeline
Usage : my \$results = \$my_object->getPipeline();
Function : Method used to get pipeline from database
Returns : Reference to a hash
:
=cut
=head2 getRibosomalRNAs
Title : getRibosomalRNAs
Usage : my \$results = \$my_object->getRibosomalRNAs( -hash => \%{ ( "pipeline_id" => "4528" ) } );
Function : Method used to get rRNAs availables in the sequence
Returns : list reference of rRNAs available
Args : named arguments:
: -hash => referenced hash with pipeline_id property
:
=cut
=head2 analyses_CDS
Title : analyses_CDS
Usage : my \$results = \$my_object->analyses_CDS( -hash => \%{ (
"pipeline" => "4528"
) } );
Function : Method used to realize search based on parameters received by form of analyses of protein-coding genes
Returns : Return a referenced hash with a list of feature IDs and total number of results
Args : named arguments:
: -hash => referenced hash with the following properties:
| Key | Description |
| :-- | :-- |
| pipeline | Scalar variable with pipeline ID |
| contig | Scalar variable with feature ID from contig |
| geneDesc | Scalar variable which realize search by all CDS with this description |
| noDesc | Scalar variable which realize search by all CDS that doesn’t have this description |
| individually | Scalar variable which make all terms from geneDesc and noDesc match |
| noGO | Scalar variable, if you don’t want to have results related to GO annotation |
| goID | Scalar variable with GO Identifier |
| goDesc | Scalar variable with GO Description |
| noTC | Scalar variable, if you don’t want to have results related to TCDB annotation |
| tcdbID | Scalar variable with TCDB ID |
| tcdbFam | Scalar variable with TCDB Family |
| tcdbSubclass | Scalar variable with TCDB subclass |
| tcdbClass | Scalar variable with TCDB class |
| tcdbDesc | Scalar variable with TCDB description |
| noBlast | Scalar variable, if you don’t want to have results related to BLAST annotations |
| blastID | Scalar variable with BLAST identifier |
| blastDesc | Scalar variable with BLAST description |
| noRps | Scalar variable, if you don’t want to have results related to RPS-BLAST annotations |
| rpsID | Scalar variable with RPS-BLAST Identifier |
| rpsDesc | Scalar variable with RPS-BLAST Description |
| noKEGG | Scalar variable, if you don’t want to have results related to KEGG annotations |
| koID | Scalar variable with KEGG Identifier |
| keggPath | Scalar variable with KEGG Pathway |
| keggDesc | Scalar variable with KEGG description |
| noOrth | Scalar variable, if you don’t want to see results related to orthology annotations. |
| orthID | Scalar variable with orthology Identifier |
| orthDesc | Scalar variable with orthology description |
| noIP | Scalar variable, if you don’t want to see results related to InterProScan annotations. |
| interproID | Scalar variable with InterProScan identifier |
| interproDesc | Scalar variable with InterProScan description |
| noTMHMM | Scalar variable, if you don’t want results related to TMHMM annotations. |
| TMHMMdom | Scalar variable with number of transmembrane domains |
| tmhmmQuant | Scalar variable which auxiliate search of TMHMMdom, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| noDGPI | Scalar variable, if you don’t want results related to DGPI annotations. |
| cleavageSiteDGPI | Scalar variable with cleavage site from DGPI |
| scoreDGPI | Scalar variable with score from DGPI |
| cleavageQuant | Scalar variable which auxiliate search of cleavageSiteDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| scoreQuant | Scalar variable which auxiliate search of scoreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| noPreDGPI | Scalar variable, if you don’t want results related to PreDGPI annotations. |
| namePreDGPI | Scalar variable with name of PreDGPI |
| positionPreDGPI | Scalar variable with position from PreDGPI |
| positionQuantPreDGPI | Scalar variable which auxiliate search of positionPreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| specificityPreDGPI | Scalar variable specifity from PreDGPI |
| specificityQuantPreDGPI | Scalar variable which auxiliate search of specificityPreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| sequencePreDGPI | Scalar variable with sequence to compare with PreDGPI annotations |
| noBigGPI | Scalar variable, if you don’t want results related to BiGPI annotations. |
| pvalueBigpi | Scalar variable value from BiGPI |
| pvalueQuantBigpi | Scalar variable which auxiliate search of quantity BiGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| positionBigpi | Scalar variable value with the position of BiGPI annotation |
| positionQuantBigpi | Scalar variable which auxiliate search of position BiGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| noPhobius | Scalar variable, if you don’t want results related to Phobius annotations. |
| TMdom | Scalar vairable, quantity of transmembrane domains |
| tmQuant | Scalar variable which auxiliate search of parameter TMdom, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| sigP | Scalar variable if you want the phobius with result with signal peptide. If you don’t care: “sigPwhatever”, if you want: “sigPyes”, if you don’t want: “sigPno” |
| pageSize | Scalar variable with the page size |
| offset | Scalar variable with the offset |
| components | Scalar variable with annotation component names used |
:
=cut
=head2 generate_clause
Method used to generate clause for any query
=cut
=head2 rRNA_search
Title : rRNA_search
Usage : my \$results = \$my_object->rRNA_search( -hash => \%{ ("pipeline" => "4528", "pageSize" => "10", "offset" => "0") } );
Function : Method used to realize search of rRNAs by contig and type
Returns : Returns a array of feature IDs of rRNA results as response
Args : named arguments:
: -hash => referenced hash with the following properties:
| Key | Descriptions |
| :-- | :-- |
| pipeline | Pipeline ID |
| pageSize | Quantity of elements |
| offset | Offset of search |
| type | Type of rRNA |
| contig | Contig ID |
:
=cut
=head2 tRNA_search
Title : tRNA_search
Usage : my \$results = \$my_object->tRNA_search( -hash => \%{ ("pipeline" => "4528") } );
Function : Method used to return tRNA data from database
Returns : Returns hash with Report_HTML_DB::Models::Application::TRNASearch list and total number of results
Args : named arguments:
: -hash => referenced hash with the following properties:
| Key | Description |
| :-- | :-- |
| pipeline | Scalar variable with pipeline ID |
| pageSize | Scalar variable with the page size |
| offset | Scalar variable with the offset |
| contig | Scalar variable with feature ID from contig |
| tRNAaa | Scalar variable to search tRNA by amino acid |
| tRNAcd | Scalar variable to search tRNA by codon |
:
=cut
=head2 trf_search
Title : trf_search
Usage : my \$results = \$my_object->trf_search( -hash => \%{ ("pipeline" => "4528") } );
Function : Method used to return tandem repeats data from database
Returns : Returns a referenced hash with Report_HTML_DB::Models::Application::TRFSearch list and total number of results available
Args : named arguments:
: -hash => referenced hash with the following properties:
| Key | Description |
| :-- | :-- |
| pipeline | Scalar variable with pipeline ID |
| pageSize | Scalar variable with the page size |
| offset | Scalar variable with the offset |
| contig | Scalar variable with feature ID from contig |
| TRFrepSeq | Scalar variable with sequence in repetition unit |
| TRFrepSize | Scalar variable with repetition units of bases |
| TRFsize | Scalar variable which auxiliate search of repetition units of bases, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| TRFrepNumMin | Scalar variable with occurrences in this min value |
| TRFrepNumMax | Scalar variable with occurrences in this max value |
=cut
=head2
Method used to return non coding RNAs data from database
=cut
=head2
Method used to return transcriptional terminator data from database
=cut
=head2
Method used to return ribosomal binding sites data from database
=cut
=head2
Method used to return horizontal transferences data from database
=cut
=head2
Method used to return the reverse complement
=cut
=head2
Method used to realize search by feature
=cut
=head2
Method used to realize search for basic content of any feature
=cut
=head2
Method used to get gene by position
=cut
=head2
Method used to realize search by subevidences
=cut
=head2
Method used to realize search by interval evidence properties
=cut
=head2
Method used to realize search by similarity evidence properties
=cut
=head2
Method used to get identifier and description of similarity
=cut
=head2
Method used to get feature ID by uniquename
=cut
=head2
Method used to get target class
=cut
=head2
Method used to get GO results from feature ID
=cut
=head1 NAME
$packageDBI - DBI Model Class
=head1 SYNOPSIS
This repository execute queries in annotation database created by EGene2
=head1 DESCRIPTION
DBI Model Class.
=head1 AUTHOR - Wendel Hime Lino Castro
Wendel Hime Lino Castro wendelhime\@hotmail.com
=head1 LICENSE
This library is free software, you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
=head1 NAME
TESTE2::Controller::Site - Catalyst Controller
=head1 DESCRIPTION
Catalyst Controller.
=head1 METHODS
=cut
=head2 getHTMLContent
Method used to get HTML content from file by filepath
=cut
=head2
Method used to return components used
=cut
=head2
Method used to get file by component id
=cut
=head2
Method used to view result by component ID
=cut
=head2
Method used to get filename by filepath
=cut
=head2 searchContig
Method used to realize search by contigs, optional return a stretch or a reverse complement
=cut
=head2 reverseComplement
Method used to return the reverse complement of a sequence
=cut
=head2 formatSequence
Method used to format sequence
=cut
=head2
Standard return of status ok
=cut
=encoding utf8
=head1 AUTHOR
Wendel Hime L. Castro,,,
=head1 LICENSE
This library is free software. You can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
=head1 NAME
services::Controller::Blast - Catalyst Controller
=head1 DESCRIPTION
Catalyst Controller.
=head1 METHODS
=cut
=head2
Method used to realize search blast
=cut
=head2
Method used to make a default return of every ok request using BaseResponse model
=cut
=encoding utf8
=head1 AUTHOR
Wendel Hime L. Castro,,,
=head1 LICENSE
This library is free software. You can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
=head1 NAME
services::Controller::SearchDatabase - Catalyst Controller
=head1 DESCRIPTION
Catalyst Controller.
=head1 METHODS
=cut
=head2 getFeatureID
Method used to get feature id
=cut
=head2
Method used to realize search of rRNA
=cut
=head2 searchGene
Method used to search on database genes
=cut
=head2 encodingCorrection
Method used to correct encoding strings come from SQLite
=cut
=head2 getGeneBasics
Method used to return basic data of genes from database: the beginning position from sequence, final position from the sequence, type, name
return a list of hash containing the basic data
=cut
=head2 getSubsequence
Method used to get subsequence stretch of gene, returning the sequence, had to return in a json!
=cut
=head2
Method used to return subevidences based on feature id
=cut
=head2
Method used to return properties of evidences that the type is interval and basic data of everything isn't CDS
=cut
=head2
Method used to return properties of evidence typed like similarity
=cut
=head2 reverseComplement
Method used to return the reverse complement of a sequence
=cut
=head2 formatSequence
Method used to format sequence
=cut
=head2 analysesCDS
Method used to make search of analyses of protein-coding genes
=cut
=head2
Method used to realize search of tRNA
=cut
=head2
Method used to get data of tandem repeats
=cut
=head2
Method used to get data of non coding RNAs
=cut
=head2
Method used to get data of transcriptional terminators
=cut
=head2
Method used to get data of ribosomal binding sites
=cut
=head2
Method used to get data of horizontal gene transfers
=cut
=head2
Method used to get feature by position
=cut
=head2
Method used to make a default return of every ok request using BaseResponse model
=cut
=encoding utf8
=head1 AUTHOR
Wendel Hime L. Castro,,,
=head1 LICENSE
This library is free software. You can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
=head1 NAME
$temporaryPackage - Catalyst Controller
=head1 DESCRIPTION
Catalyst Controller.
=head1 METHODS
=cut
=head2
Standard return of status ok
=cut
=encoding utf8
=head1 AUTHOR
Wendel Hime L. Castro,,,
=head1 LICENSE
This library is free software. You can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
=head1 NAME
$temporaryPackage - Catalyst Controller
=head1 DESCRIPTION
Catalyst Controller.
=head1 METHODS
=cut
=head2
Standard return of status ok
=cut
=encoding utf8
=head1 AUTHOR
Wendel Hime L. Castro,,,
=head1 LICENSE
This library is free software. You can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
=encoding utf-8
=head1 NAME
$temporaryPackage - Root Controller for $html_dir
=head1 DESCRIPTION
Root where will have the main pages
=head1 METHODS
=cut
=head2 globalAnalyses
Global analyses page
=cut
=head2 searchDatabase
Search database page (/SearchDatabase)
=cut
=head2 about
About page (/About)
=cut
=head2 blast
The blast page (/Blast)
=cut
=head2 downloads
The download page (/Downloads)
=cut
=head2 encodingCorrection
Method used to correct encoding strings come from SQLite
=cut
=head2
Method used to get feature id
=cut
=head2 help
The help page (/Help)
=cut
=head2 index
The root page (/)
=cut
=head2 reverseComplement
Method used to return the reverse complement of a sequence
=cut
=head2 formatSequence
Method used to format sequence
=cut
=head2 default
Standard 404 error page
=cut
=head2 renderView
Attempt to render a view, if needed.
=cut
=head1 AUTHOR
Wendel Hime L. Castro,,,
=head1 LICENSE
This library is free software. You can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
=head2
Method used to get content of TCDB file
@param tcdb_file => filepath
return sql to be used
=cut
=head2
Method used to get code number of the product
@param subject_id
return list with code number and product
=cut
=head2 reverseComplement
Method used to return the reverse complement of a sequence
=cut
=head2 formatSequence
Method used to format sequence
=cut
=head2 verify_element
Method used to verify if element exists in list reference
=cut
=head2
Method used to get filename by filepath
=cut
=head1 NAME
report_html_db.pl - Generate a dynamic web page based on EGene2 database results.
=head1 DESCRIPTION
Responsible for generation of applications like website and services that allow users to access dynamic pages with the possibility to realize a complex query with the database of annotations created as a result of execution of pipelines by the platform EGene2, execute BLAST searches, and turn available annotation files and results.
=head1 SYNOPSIS
$ Report_HTML_DB
report_html_db.pl
=head1 AUTHOR
Wendel Hime Lino Castro
=head1 LICENSE
GNU General Public License v3.0
=head1 INSTALLATION
Using C<cpan>:
$ cpan Report_HTML_DB
Manual install:
$ perl Makefile.PL
$ make
$ make install
=cut