getPipeline

Title    : getPipeline
Usage    : my \$results = \$my_object->getPipeline();
Function : Method used to get pipeline from database
Returns  : Reference to a hash
         :

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
         :

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 |            
         :

generate_clause

Method used to generate clause for any query

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 |

         :

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 |           
         :

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 |

Method used to return non coding RNAs data from database

Method used to return transcriptional terminator data from database

Method used to return ribosomal binding sites data from database

Method used to return horizontal transferences data from database

Method used to return the reverse complement

Method used to realize search by feature

Method used to realize search for basic content of any feature

Method used to get gene by position

Method used to realize search by subevidences

Method used to realize search by interval evidence properties

Method used to realize search by similarity evidence properties

Method used to get identifier and description of similarity

Method used to get feature ID by uniquename

Method used to get target class

Method used to get GO results from feature ID

NAME

$packageDBI - DBI Model Class 

SYNOPSIS

This repository execute queries in annotation database created by EGene2

DESCRIPTION

DBI Model Class.

AUTHOR - Wendel Hime Lino Castro

Wendel Hime Lino Castro wendelhime\@hotmail.com

LICENSE

This library is free software, you can redistribute it and/or modify it under the same terms as Perl itself.

NAME

TESTE2::Controller::Site - Catalyst Controller

DESCRIPTION

Catalyst Controller.

METHODS

getHTMLContent Method used to get HTML content from file by filepath

Method used to return components used

Method used to get file by component id

Method used to view result by component ID

Method used to get filename by filepath

searchContig

Method used to realize search by contigs, optional return a stretch or a reverse complement

reverseComplement

Method used to return the reverse complement of a sequence

formatSequence

Method used to format sequence

Standard return of status ok

AUTHOR

Wendel Hime L. Castro,,,

LICENSE

This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.

NAME

services::Controller::Blast - Catalyst Controller

DESCRIPTION

Catalyst Controller.

METHODS

Method used to realize search blast

Method used to make a default return of every ok request using BaseResponse model

AUTHOR

Wendel Hime L. Castro,,,

LICENSE

This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.

NAME

services::Controller::SearchDatabase - Catalyst Controller

DESCRIPTION

Catalyst Controller.

METHODS

getFeatureID

Method used to get feature id

Method used to realize search of rRNA

searchGene

Method used to search on database genes

encodingCorrection

Method used to correct encoding strings come from SQLite

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

getSubsequence

Method used to get subsequence stretch of gene, returning the sequence, had to return in a json!

Method used to return subevidences based on feature id

Method used to return properties of evidences that the type is interval and basic data of everything isn't CDS

Method used to return properties of evidence typed like similarity

reverseComplement

Method used to return the reverse complement of a sequence

formatSequence

Method used to format sequence

analysesCDS

Method used to make search of analyses of protein-coding genes

Method used to realize search of tRNA

Method used to get data of tandem repeats

Method used to get data of non coding RNAs

Method used to get data of transcriptional terminators

Method used to get data of ribosomal binding sites

Method used to get data of horizontal gene transfers

Method used to get feature by position

Method used to make a default return of every ok request using BaseResponse model

AUTHOR

Wendel Hime L. Castro,,,

LICENSE

This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.

NAME

$temporaryPackage - Catalyst Controller

DESCRIPTION

Catalyst Controller.

METHODS

Standard return of status ok

AUTHOR

Wendel Hime L. Castro,,,

LICENSE

This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.

NAME

$temporaryPackage - Catalyst Controller

DESCRIPTION

Catalyst Controller.

METHODS

Standard return of status ok

AUTHOR

Wendel Hime L. Castro,,,

LICENSE

This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.

NAME

$temporaryPackage - Root Controller for $html_dir

DESCRIPTION

Root where will have the main pages

METHODS

globalAnalyses

Global analyses page

searchDatabase

Search database page (/SearchDatabase)

about

About page (/About)

blast

The blast page (/Blast)

downloads

The download page (/Downloads)

encodingCorrection

Method used to correct encoding strings come from SQLite

Method used to get feature id

help

The help page (/Help)

index

The root page (/)

reverseComplement

Method used to return the reverse complement of a sequence

formatSequence

Method used to format sequence

default

Standard 404 error page

renderView

Attempt to render a view, if needed.

AUTHOR

Wendel Hime L. Castro,,,

LICENSE

This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.

Method used to get content of TCDB file @param tcdb_file => filepath return sql to be used

Method used to get code number of the product @param subject_id return list with code number and product

reverseComplement

Method used to return the reverse complement of a sequence

formatSequence

Method used to format sequence

verify_element

Method used to verify if element exists in list reference

Method used to get filename by filepath

NAME

report_html_db.pl - Generate a dynamic web page based on EGene2 database results.

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.

SYNOPSIS

$ Report_HTML_DB
report_html_db.pl

AUTHOR

Wendel Hime Lino Castro

LICENSE

GNU General Public License v3.0

INSTALLATION

Using cpan:

$ cpan Report_HTML_DB

Manual install:

$ perl Makefile.PL
$ make
$ make install

cpanm Report_HTML_DB

perl -MCPAN -e shell
install Report_HTML_DB