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Repositories
Repositories package was developed thinking in centralize functions which can be used by another applications, if you need to change something programmatically, you should change this package. This package is composed by two objects:
SearchDatabaseRepository is located in Organism-Service/lib/Organism/Service/Model/SearchDatabaseRepository.pm, in other words, SearchDatabaseRepository is created by report_html_db.pl script when he's executed.
Report_HTML_DB::Repositories::BlastRepository run programs from BLAST+ package and fancy_blast.pl from EGene2
Execute similarity search using BLAST tool, mount a command line and execute Return a list reference with search result.
| Parameters | Description |
|---|---|
| $self | scalar instance BlastRepository it self |
| $program | scalar with the name of the program |
| $database | scalar with the database |
| $fastaSequence | scalar with the sequence |
| $from | scalar from position sequence |
| $to | scalar to position sequence |
| $filter | referenced list with filters |
| $expect | scalar with the expected evalue |
| $matrix | scalar with matrix |
| $ungappedAlignment | scalar with off or on for ungapped alignments |
| $geneticCode | scalar with the genetic code |
| $databaseGeneticCode | scalar with the database genetic code |
| $frameShiftPenality | scalar with the frame shift penality option |
| $alignmentView | scalar with the alignment view |
| $descriptions | scalar with the quantity of descriptions |
| $alignments | scalar with the quantity of alignments |
| $costOpenGap | scalar with the cost to open gap |
| $costToExtendGap | scalar with the cost to extend a gap |
| $wordSize | scalar with the word size |
Execute fancy_blast.pl using BLAST result and generate a HTML file with image links
Return 0 for bad status and 1 for everything ok, the file and image was created
| Parameters | Description |
|---|---|
| $self | Scalar instance BlastRepository it self |
| $blast | Scalar variable with filepath to BLAST results |
| $output | Scalar variable with filepath to output result from fancy_blast.pl |
| $database | Scalar variable with database code(isn't required |
This repository execute queries in annotation database created by EGene2
Method used to get pipeline ID from database Return a hash reference with pipeline_id property
Method used to get rRNAs available in the sequence
Return a list reference of rRNAs available
The next table, illustrates keys and descriptions which compose the hash reference $hash
| Key | Description |
|---|---|
| pipeline | Pipeline ID |
Method used to realize search of rRNAs by contig and type
Returns a array of feature IDs of rRNA results as response
The next table, illustrates keys and descriptions which compose the hash reference $hash
| Key | Descriptions |
|---|---|
| pipeline | Pipeline ID |
| pageSize | Quantity of elements |
| offset | Offset of search |
| type | Type of rRNA |
| contig | Contig ID |
Method used to get feature ID by uniquename
Return feature ID
| Parameters | Description |
|---|---|
| uniquename | Uniquename from feature |
Method used to realize search by feature
Return a hash with Report_HTML_DB::Models::Application::Feature list and total number of values
| Parameters | Description |
|---|---|
| pipeline | Pipeline ID |
| geneID | Search by genes with this locus tag |
| geneDescription | Search by genes with this description |
| noDescription | Search by genes which don't contain this description |
| individually | Match all terms, positive values can be "on", 1; set 0 if you don't want |
| featureId | Search by a list of genes with those feature ID; Should be a string with feature IDs separated by spaces |
| pageSize | Quantity of elements |
| offset | Offset of search |
Method used to realize search by basic content of any feature Return a referenced list of Report_HTML_DB::Models::Application::Feature
| Parameters | Description |
|---|---|
| id | Feature ID |
| pipeline | Pipeline ID |
Method used to realize search by subevidences Return a referenced list of Report_HTML_DB::Models::Application::Subevidence
| Parameters | Description |
|---|---|
| feature | Feature ID |
Method used to realize search based on parameters received by form of analyses of protein-coding genes Return a referenced hash with a list of feature IDs and total number of results
| 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 get a list of annotated tRNAs
Returns hash with Report_HTML_DB::Models::Application::TRNASearch list and total number of results
The following table list key-value hash table parameters:
| 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 |
Method used to return tandem repeats data from database
Returns a referenced hash with Report_HTML_DB::Models::Application::TRFSearch list and total number of results available
The following table list key-value hash table parameters:
| 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
Returns a referenced hash with Report_HTML_DB::Models::Application::NcRNASearch list and total number of results available
The following table list key-value hash table parameters:
| 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 |
| ncRNAtargetID | Scalar variable with target ID from RFAM |
| ncRNAevalue | Scalar variable with evalue from result |
| ncRNAevM | Scalar variable which auxiliate search with evalue result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| ncRNAtargetName | Scalar variable with target name |
| ncRNAtargetClass | Scalar variable with target class |
| ncRNAtargetType | Scalar variable with target type |
| ncRNAtargetDesc | Scalar variable with target description |
Method used to return transcriptional terminator data from database
Returns a referenced hash with Report_HTML_DB::Models::Application::TranscriptionalTerminator list and total number of results available
The following table list key-value hash table parameters:
| 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 |
| TTconf | Scalar variable with transcriptional termintators with confidence score |
| TTconfM | Scalar variable which auxiliate search with confidence score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| TThp | Scalar variable with transcriptional terminators with hairpin score |
| TThpM | Scalar variable which auxiliate search with hairpin score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| TTtail | Scalar variable with transcriptional terminators with tail score |
| TTtailM | Scalar variable which auxiliate search with tail score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
Method used to return ribosomal binding sites data from database
Returns a referenced hash with Report_HTML_DB::Models::Application::RBSSearch list and total number of results avilable
The following table list key-value hash table parameters:
| 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 |
| RBSpattern | Scalar variable with a sequence pattern |
| RBSshift | Scalar variable with "on" for true value or 0 for false, represents a search for all ribosomal binding site predictions that recommend a shift in start codon position |
| RBSshiftM | Scalar variable with option values, if you want upstream, value should be "neg"; if you want downstream, value should be "pos"; if you want either, value should be "both" |
| RBSnewcodon | Scalar variable with "on" for true value or 0 for false, represents a search for all ribosomal binding site predictions that recommend a change of start codon |
Method used to return horizontal transferences data from database
Returns a referenced hash with Report_HTML_DB::Models::Application::AlienHunterSearch list and total number of results available
The following table list key-value hash table parameters:
| 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 |
| AHlen | Scalar variable with length of regions predicted |
| AHlenM | Scalar variable which auxiliate search with length of regions predicted result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| AHscore | Scalar variable with value to get regions of score |
| AHscM | Scalar variable which auxiliate search with regions of score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
| AHthr | Scalar variable with value to get regions of threshold |
| AHthrM | Scalar variable which auxiliate search with regions of treshold result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none" |
Method used to get gene by position
Returns a referenced hash with a feature ID's list and total number of results avilable
The following table list key-value hash table parameters:
| Parameters | Description |
|---|---|
| start | Start position |
| end | End position |
| 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 |
Method used to get target class
Returns a referenced list of target classes values
| Parameters | Description |
|---|---|
| pipeline_id | Pipeline ID |
Method used to realize search by similarity evidence properties
Returns a referenced hash with properties keys and values
| Parameters | Description |
|---|---|
| feature_id | Feature ID |
Method used to get identifier and description of similarity
Returns a referenced hash composed by identifier and description
| Parameters | Description |
|---|---|
| feature_id | Feature ID |
Method used to realize search by interval evidence properties
Returns a referenced list with referenced hashes of keys and values properties
| Parameters | Description |
|---|---|
| feature_id | Feature ID |
Method used to get GO results from feature ID
Returns a referenced list of GO results annotated
| Parameters | Description |
|---|---|
| pipeline_id | Pipeline ID |
| feature_id | Feature ID |
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Getting started
1.1 Setup
1.2 Running
- Configuration files
2.1 Creating config file
2.2 Creating JSON file for Website pages
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Developers Documentation
3.1 Services API
3.2 Website
3.3 Report_HTML_DB -
Deploy
4.1 Considerations
4.2 Apache
4.3 Docker
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Questions and feedback