## utilities.BlastUtils Usage ``` python utilities.BlastUtils() ``` ## Methods | Name | Description | |----|----| | [__init__()](#__init__) | Various utilities to help with blast specific functionality. | | [accession_csv2sqlite()](#accession_csv2sqlite) | Convert am OrthoEvol csv accession file to an sqlite3 database. | | [accession_sqlite2pandas()](#accession_sqlite2pandas) | Convert a sqlite3 database with an OrthoEvol accession table to a pandas dataframe. | | [analyze_duplicate_accessions()](#analyze_duplicate_accessions) | Classify duplicate accessions and calculate report counts once. | | [gene_list_config()](#gene_list_config) | Create or use a blast configuration file (accession file). | | [get_dup_acc()](#get_dup_acc) | Get duplicated accession numbers during post-blast analysis. | | [get_miss_acc()](#get_miss_acc) | Get missing accession numbers during post-blast analysis. | | [map_func()](#map_func) | Format/parse hit ids generated from blast xml results. | | [my_gene_info()](#my_gene_info) | Use Biothings' MyGene api to get information about genes. | | [paml_org_formatter()](#paml_org_formatter) | Take a list of organisms and format each organism name for PAML, | ------------------------------------------------------------------------ #### \_\_init\_\_() Various utilities to help with blast specific functionality. Usage ``` python __init__() ``` ------------------------------------------------------------------------ #### accession_csv2sqlite() Convert am OrthoEvol csv accession file to an sqlite3 database. Usage ``` python accession_csv2sqlite(acc_file, table_name, db_name, path) ``` ##### Parameters `acc_file: str` The name of the accession file. The file name is used to create a table in the sqlite3 database. Any periods will be replaced with underscores. `table_name: str` The name of the table in the database. `db_name: str` The name of the new database. `path: str` The relative path of the csv file and the database. ------------------------------------------------------------------------ #### accession_sqlite2pandas() Convert a sqlite3 database with an OrthoEvol accession table to a pandas dataframe. Usage ``` python accession_sqlite2pandas(table_name, db_name, path, exists=True, acc_file=None) ``` ##### Parameters `table_name: str` Name of the table in the database. `db_name: str` The name of the new database. `path: str` The relative path of the csv file and the database. `exists: bool = ``True` A flag used to create a database if needed. `acc_file: str | None = None` The name of the accession file. The file name is used to create a table in the sqlite3 database. Any periods will be replaced with underscores. ##### Returns `pd.DataFrame` A pandas DataFrame containing the accession data. ------------------------------------------------------------------------ #### analyze_duplicate_accessions() Classify duplicate accessions and calculate report counts once. Usage ``` python analyze_duplicate_accessions(acc_dict, gene_list, org_list) ``` ------------------------------------------------------------------------ #### gene_list_config() Create or use a blast configuration file (accession file). Usage ``` python gene_list_config(file, data_path, gene_list, taxon_dict, logger) ``` This function configures different files for new BLASTS. It also helps recognize whether or not a BLAST was terminated in the middle of the workflow. This removes the last line of the accession file if it is incomplete. ##### Parameters `file: str.` An accession file to analyze. `data_path: str.` The path of the accession file. `gene_list: list.` A gene list in the same order as the accession file. `taxon_dict: dict.` A taxon id dictionary for logging purposes. `logger: LogIt.` A LogIt logger for logging. ##### Returns Returns a continued gene_list to pick up from an interrupted Blast. ------------------------------------------------------------------------ #### get_dup_acc() Get duplicated accession numbers during post-blast analysis. Usage ``` python get_dup_acc(acc_dict, gene_list, org_list) ``` ##### Parameters `acc_dict: Mapping[str, Sequence[Sequence[str]]]` A dictionary with accession numbers as keys, and a gene/organism list as values. `gene_list: Sequence[str]` A full list of genes. `org_list: Sequence[str]` A full list of organisms. ##### Returns `dict.` A master duplication dictionary used to initialize the duplicate class variables. ------------------------------------------------------------------------ #### get_miss_acc() Get missing accession numbers during post-blast analysis. Usage ``` python get_miss_acc(acc_dataframe) ``` ##### Parameters `acc_dataframe: pd.DataFrame` A pandas dataframe containing the accession csv file data(post BLAST). ##### Returns `dict.` A dictionary with data about the missing accession numbers by Gene and by Organism. ------------------------------------------------------------------------ #### map_func() Format/parse hit ids generated from blast xml results. Usage ``` python map_func(hit) ``` ##### Parameters `hit: Bio.SearchIO.HSP | Bio.SearchIO.Hit` A BLAST hit object from SearchIO. ##### Returns `Bio.SearchIO.HSP | Bio.SearchIO.Hit` The hit object with formatted id, id1 (accession), and id2 (gi). ------------------------------------------------------------------------ #### my_gene_info() Use Biothings' MyGene api to get information about genes. Usage ``` python my_gene_info(acc_dataframe, blast_query="Homo_sapiens") ``` ##### Parameters `acc_dataframe: pd.DataFrame.` A pandas dataframe containing the accession csv file data. `blast_query: str. = ``"Homo_sapiens"` The query organism for used during Blasting. ##### Returns `pd.DataFrame.` Returns a data-frame with hot data about each gene. ------------------------------------------------------------------------ #### paml_org_formatter() Take a list of organisms and format each organism name for PAML, Usage ``` python paml_org_formatter(organisms) ``` which can only take names that are less than a certain length (36 characters?). ##### Parameters `organisms: list` A list of organisms. ##### Returns `list` A list of formatted organism names for PAML.