Gene_search

NetExplorer.views.pages.gene_search.gene_search(request)

Search for planarian genes and transcripts using their identifiers or any of their annotations (PFAM, GO, homologs).

Accepts:

• GET

Parameters

• genesymbol (str) – Search term with gene symbol(s).

• database (str) – Database in which to search for gene symbol(s).

Response:

• res (list of Nodes): Results to be displayed.

• summary (str): Summary of the search.

• search_error (int): Indicates if there was an error in the search.

• valid_query (bool): Indicates if query is valid.

Template:

• NetExplorer/gene_search.html

NetExplorer.views.pages.gene_search.get_search_summary(datasets, results)

Cretes a summary of the searched performed in gene_search.

Parameters

• datasets (list of str) – List of all datasets to which User has permissions to.

• results (list of Node) – List of Node objects that match the serach.

Returns

List of tuples with each one of them having the name of the Dataset and the second having the number of hits for that dataset.

Return type

list of tuple

NetExplorer.views.pages.gene_search.sort_results(datasets, results)

Sorts gene/node results by:

1- Dataset (Smesgene - Human - AllContigs by year) 2- Gene Name. 3- Contig/Gene symbol.

Also removes results from not allowed datasets.

Parameters

• datasets (list of Dataset) – list of allowed Datasets.

• results (GraphCytoscape) – GraphCytoscape of search results to sort.

Returns

Lists of tuples. Each tuple has (dataset, node name, node symbol).

Return type

list of tuple