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Clients
Clients package represents a communication layer between any application and a REST endpoint to a Service application. There is two clients available:
This class provide functions that allows a communication with the Service application, standarzing requests of BLAST functions
| Property | Description |
|---|---|
| rest_endpoint | REST endpoint URL |
Receives a hash reference and stringify them to return like parameters URL
Return a string with URL parameters
Create a request
Return content response
| Parameters | Description |
|---|---|
| rest_endpoint | REST endpoint to Service application |
| action | Action to be executed |
| parameters | A hash reference of parameters to be stringified |
| method | Method to execute request(POST, GET) |
Execute a request of BLAST search in Service application
Returns a Report_HTML_DB::Models::Services::BaseResponse
The next table, it's a demonstration of key values to parameters
| Key | Value |
|---|---|
| PROGRAM | Program name (blastn, blastp, blastx, tblastn, tblastx) |
| DATALIB | Data lib(PMN_genome_1 for all genes - nucleotidic sequences, PMN_genes_1 for contigs in nucleotidic sequence, PMN_prot_1 for protein sequences) |
| QUERY_FROM | Set subsequence from |
| QUERY_TO | Set subsequence to |
| FILTER | Set filters(for low complexity use "L" value) |
| EXPECT | Read more here |
| MAT_PARAM | Read more here |
| UNGAPPED_ALIGNMENT | "is_set" if you want a ungapped alignment |
| GENETIC_CODE | Read more here |
| DB_GENETIC_CODE | Read more here |
| COST_OPEN_GAP | Read more here |
| COST_EXTEND_GAP | Read more here |
| WORD_SIZE | Word size for wordfinder algorithm (length of best perfect match) |
| ALIGNMENT_VIEW | Read more here |
| DESCRIPTIONS | Read more here |
| ALIGNMENTS | Read more here |
Create a request to Service application asking to run fancy_blast.pl with BLAST result Returns a Report_HTML_DB::Models::Services::BaseResponse
| Parameters | Description |
|---|---|
| blast | blast result as a string |
This class provide functions that allows a communication with the Service application, standarzing requests for search database actions
| Property | Description |
|---|---|
| rest_endpoint | REST endpoint URL |
Receives a hash reference and stringify them to return like parameters URL
Return a string with URL parameters
Create a request
Return content response
| Parameters | Description |
|---|---|
| rest_endpoint | REST endpoint to Service application |
| action | Action to be executed |
| parameters | A hash reference of parameters to be stringified |
| method | Method to execute request(POST, GET) |
Method used to get pipeline ID
Returns a Report_HTML_DB::Models::Services::BaseResponse with pipeline_id as response
Method used to get ribosomal RNAs from database
Returns a Report_HTML_DB::Models::Services::BaseResponse with a list of ribosomal RNAs available on database response.
| Parameters | Description |
|---|---|
| pipeline | Pipeline ID |
Method used to request a search for rRNA
Returns a Report_HTML_DB::Models::Services::PagedResponse with array of feature IDs of rRNA results as response
The next table, illustrates keys and descriptions which compose the hash reference $parameters
| Key | Descriptions |
|---|---|
| pipeline | Pipeline ID |
| pageSize | Quantity of elements |
| offset | Offset of search |
| type | Type of rRNA |
| contig | Contig ID |
Method used to request feature ID by uniquename
Returns a Report_HTML_DB::Models::Services::BaseResponse with feature ID as response
| Parameters | Description |
|---|---|
| uniquename | Uniquename from feature |
getGene($self, $pipeline, $geneID, $geneDescription, $noDescription, $individually, $featureId, $pageSize, $offset, $contig)
Method used to get Genes
Returns a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::Feature as response
| 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 return basic data of genes from database: the beginning position from sequence, final position from the sequence, type, name
Returns a Report_HTML_DB::Models::Services::BaseResponse with a list of Report_HTML_DB::Models::Application::Feature as response.
| Parameters | Description |
|---|---|
| id | Feature ID |
| pipeline | Pipeline ID |
Method used to get subsequence stretch of gene
Returns a Report_HTML_DB::Models::Services::BaseResponse with a subsequence string as response
| Parameters | Description |
|---|---|
| type | Type of sequence (CDS, or anything else) |
| contig | Contig's name, if you're using a type of sequence different of "CDS", contig's name is required |
| sequenceName | Sequence's name, if you're using a type of sequence equal "CDS", sequence's name is required |
| start | Start position |
| end | End position |
| pipeline | Pipeline ID |
Method used to get subevidences by feature ID and pipeline ID
Returns a Report_HTML_DB::Models::Services::BaseResponse with a list of Report_HTML_DB::Models::Application::Subevidence as response
| Parameters | Description |
|---|---|
| feature | Feature ID |
| pipeline | Pipeline ID |
Method used to realize search of analyses of protein-coding genes
Returns a Report_HTML_DB::Models::Services::PagedResponse with a list of feature IDs as response
The following table list key-value hash table parameters:
| 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 tRNA annotated
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::TRNASearch as response
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 get a list of tandem repeats annotated by annotation_trf.pl
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::TRFSearch as response
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 |
Execute a GET request, asking for non coding RNAs
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::NcRNASearch as response
The next table, illustrates keys and descriptions which compose the hash reference $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 |
Execute a GET request, asking by transcriptional terminators annotations
Return a Report_HTML_DB::Models::Services::PagedResponse with Report_HTML_DB::Models::Application::TranscriptionalTerminator as response
The next table, illustrates keys and descriptions which compose the hash reference $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" |
Execute a GET request, asking by ribosomal binding sites annotation
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::RBSSearch as response.
The next table, illustrates keys and descriptions which compose the hash reference $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 |
Execute a GET request, asking by horizontal transferences annotations
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::AlienHunterSearch as response
The next table, illustrates keys and descriptions which compose the hash reference $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" |
Execute a GET request, asking for genes by position Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::Feature as response
| 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 |
Execute a GET request, asking by target classes in database
Return a Report_HTML_DB::Models::Services::BaseResponse with a list of target classes as response
| Parameters | Description |
|---|---|
| pipeline_id | Pipeline ID |
Execute a GET request, asking by similarity evidence properties from a evidence Return a Report_HTML_DB::Models::Services::BaseResponse with a hash of properties as response
| Parameters | Description |
|---|---|
| feature_id | Feature ID from evidence |
Execute a GET request, asking by identifier and description from a similarity evidence Return a Report_HTML_DB::Models::Services::BaseResponse with a hash composed by identifier and description properties, as response
| Parameters | Description |
|---|---|
| feature_id | Feature ID from evidence |
Execute a GET request, asking by interval evidence properties from a evidence Return a Report_HTML_DB::Models::Services::BaseResponse with a list of hashs composed by key and values as a response
| Parameters | Description |
|---|---|
| feature | Feature ID from evidence |
| typeFeature | Component name |
| pipeline | Pipeline ID |
Execute a GET request, asking by GO results based on feature ID Return a Report_HTML_DB::Models::Services::BaseResponse with a list of GO results as response
| 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