## Orthologs.Blast.BaseComparativeGenetics Base class in the Blast module. Usage ``` python Orthologs.Blast.BaseComparativeGenetics( project=None, project_path=os.getcwd(), acc_file=None, taxon_file=None, ref_species=None, pre_blast=False, post_blast=True, hgnc=False, proj_mana=None, copy_from_package=False, **kwargs ) ``` ## Methods | Name | Description | |----|----| | [__init__()](#__init__) | This is the base class for the Blast module. | | [get_acc_dict()](#get_acc_dict) | Input a list of accession numbers and return a dictionary with corresponding genes/organisms. | | [get_accession()](#get_accession) | Access a single accession number. | | [get_file_list()](#get_file_list) | Turn csv column to list. | | [get_hgnc_gene_info()](#get_hgnc_gene_info) | Return HGNC records in the same order as the requested symbols. | | [get_master_lists()](#get_master_lists) | Populate the organism and gene lists with a data frame. | | [get_orthologous_accessions()](#get_orthologous_accessions) | Take a single gene & return a list of accession numbers for the different orthologs. | | [get_orthologous_gene_sets()](#get_orthologous_gene_sets) | Access a list of accession numbers. | | [get_taxon_dict()](#get_taxon_dict) | Get the taxonomy information about each organism using ETE3. | | [get_tier_frame()](#get_tier_frame) | Organize a dictionary by tier. | ------------------------------------------------------------------------ #### \_\_init\_\_() This is the base class for the Blast module. Usage ``` python __init__( project=None, project_path=os.getcwd(), acc_file=None, taxon_file=None, ref_species=None, pre_blast=False, post_blast=True, hgnc=False, proj_mana=None, copy_from_package=False, **kwargs ) ``` It parses an accession file in order to provide easy handling for data. The .csv accession file contains the following header info: \* "Tier" - User defined. \* "Gene" - HUGO Gene Nomenclature Committee(HGNC) symbol for the genes of interest. \* Query Organism - A well annotated query organism. \* Other organisms - The other headers are Genus_species of other taxa. The organisms are taken from: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/multiprocessing/ The genes are taken from: http://www.guidetopharmacology.org/targets.jsp. The API gives the user access to their data in a higher level for downstream processing or for basic observation of the data. ##### Parameters `project: str | None = None` The name of the project. `project_path: str | Path | None = os.getcwd()` The location of the project, which is generally defined by the ProjectManagement configuration. `acc_file: str | None = None` The name of the accession file. `taxon_file: str | Path | None = None` A file that contains an ordered list of taxonomy ids. `ref_species: str | None = None` A reference species or organism for the blast query. `pre_blast: bool = ``False` A flag that gives the user access to an API that contains extra information about their genes using the mygene package. `post_blast: bool = ``True` A flag that is used to handle a BLAST result file, which returns information about misssing data, duplicates, etc. `hgnc: bool | str | Path = ``False` Enable HGNC annotation with the current complete dataset, or provide a local HGNC TSV path or alternate URL. `proj_mana: ProjectManagement | dict[str, Any] | None = None` This parameter is used to compose (vs inherit) the ProjectManagement class with the ComparativeGenetics class. This parameter allows the various blast classes to function with or without the Manager module. `copy_from_package: bool = ``False` Copy a packaged accession file into the project. `kwargs: Any = {}` The kwargs here are generally used for standalone blasting or for development. ##### Returns `None` A pandas data-frame, pivot-table, and associated lists and dictionaries. ------------------------------------------------------------------------ #### get_acc_dict() Input a list of accession numbers and return a dictionary with corresponding genes/organisms. Usage ``` python get_acc_dict() ``` ##### Returns An accession dictionary who's values are nest gene/organism lists. ------------------------------------------------------------------------ #### get_accession() Access a single accession number. Usage ``` python get_accession(gene, organism) ``` ##### Parameters `gene` An input gene. `organism` An input organism. ##### Returns A single accession number of the target gene/organism. ------------------------------------------------------------------------ #### get_file_list() Turn csv column to list. Usage ``` python get_file_list(file) ``` ##### Parameters `file` Name of csv file. ------------------------------------------------------------------------ #### get_hgnc_gene_info() Return HGNC records in the same order as the requested symbols. Usage ``` python get_hgnc_gene_info(gene_symbols, source=HGNC_COMPLETE_SET_URL) ``` ------------------------------------------------------------------------ #### get_master_lists() Populate the organism and gene lists with a data frame. Usage ``` python get_master_lists(df, csv_file=None) ``` It will also populate pre-blast attributes (mygene) and post-blast attributes (missing and duplicates) under the proper conditions. ##### Parameters `df` The preferred way of utilizing the function is with a data-frame. `csv_file=None` If a csv_file is given, then a data-frame will be created by reinitializing the object. (Default value = None) ##### Returns An API can be utilized to access a gene list, organism list, taxon-id list, tier list/dict/data-frame, accession list/data-frame, blast query list, mygene information, and missing/duplicate information. ------------------------------------------------------------------------ #### get_orthologous_accessions() Take a single gene & return a list of accession numbers for the different orthologs. Usage ``` python get_orthologous_accessions(gene) ``` ##### Parameters `gene` An input gene from the accession file. ##### Returns A list of accession numbers that correspond to the orthologs of the target gene. ------------------------------------------------------------------------ #### get_orthologous_gene_sets() Access a list of accession numbers. Usage ``` python get_orthologous_gene_sets(go_list=None) ``` ##### Parameters `go_list=None` A nested list of gene/organism lists (go_list = \[\[gene.1, org.1\], … , \[gene.n, org.n\]\]). (Default value = None) ##### Returns An ordered list of accession numbers (or "missing") that correspond to the go_list index. ------------------------------------------------------------------------ #### get_taxon_dict() Get the taxonomy information about each organism using ETE3. Usage ``` python get_taxon_dict() ``` ##### Returns Returns several dictionaries. One is a basic organism (key) to taxonomy id (value) dictionary, and the other is a lineage dictionary with the an organism key and a lineage dictionary as the value. The lineage dictionary keys for each organism are \["class", "family", "genus", "kingdowm", "order", "phylum", "species", "superkingdom"\]. ------------------------------------------------------------------------ #### get_tier_frame() Organize a dictionary by tier. Usage ``` python get_tier_frame(tiers=None) ``` Each tier (key) has a value, which is a data-frame of genes associated with that tier. ##### Parameters `tiers=None` A list of tiers in the accession file. (Default value = None) ##### Returns A nested dictionary for accessing information by tier.