Title : getPipeline Usage : my \$results = \$my_object->getPipeline(); Function : Method used to get pipeline from database Returns : Reference to a hash :
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 :
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 | :
Method used to generate clause for any query
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 | :
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 | :
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
$packageDBI - DBI Model Class
This repository execute queries in annotation database created by EGene2
DBI Model Class.
Wendel Hime Lino Castro wendelhime\@hotmail.com
This library is free software, you can redistribute it and/or modify it under the same terms as Perl itself.
TESTE2::Controller::Site - Catalyst Controller
Catalyst Controller.
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
Method used to realize search by contigs, optional return a stretch or a reverse complement
Method used to return the reverse complement of a sequence
Method used to format sequence
Wendel Hime L. Castro,,,
This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.
services::Controller::Blast - Catalyst Controller
Method used to realize search blast
Method used to make a default return of every ok request using BaseResponse model
services::Controller::SearchDatabase - Catalyst Controller
Method used to get feature id
Method used to realize search of rRNA
Method used to search on database genes
Method used to correct encoding strings come from SQLite
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
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
$temporaryPackage - Catalyst Controller
$temporaryPackage - Root Controller for $html_dir
Root where will have the main pages
Global analyses page
Search database page (/SearchDatabase)
About page (/About)
The blast page (/Blast)
The download page (/Downloads)
The help page (/Help)
The root page (/)
Standard 404 error page
Attempt to render a view, if needed.
Method used to verify if element exists in list reference
report_html_db.pl - Generate a dynamic web page based on EGene2 database results.
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.
$ Report_HTML_DB report_html_db.pl
Wendel Hime Lino Castro
GNU General Public License v3.0
Using cpan:
cpan
$ cpan Report_HTML_DB
Manual install:
$ perl Makefile.PL $ make $ make install
2 POD Errors
The following errors were encountered while parsing the POD:
=pod directives shouldn't be over one line long! Ignoring all 4 lines of content
Non-ASCII character seen before =encoding in 'doesn’t'. Assuming UTF-8
To install Report_HTML_DB, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Report_HTML_DB
CPAN shell
perl -MCPAN -e shell install Report_HTML_DB
For more information on module installation, please visit the detailed CPAN module installation guide.