![]() ![]() Retrieving protein data for CAZy classes and families to scrape.Additional operations to fine tune how cazy_webscraper operates.Using a configuration and the command-line.Combining CAZy class, CAZy family and taxonomy filters.Enabling retrieving subfamily annotations.Specifying CAZy classes and families to scrape.Options configurable at the command line.To run slowly but this may be due to bandwidth at the database server, or server speed.Ĭazy_webscraper provides a progress bar to reassure the user that the webscraper is working. When using cazy_webscraper to retrieve data from UniProt, NCBI or PDB, the webscraper can appear This is typically at the weekend and overnight. When performing a series of many automated, repeated calls to a server it is polite to do this when internet traffic is lowest at the server. To interrogate the database, use the cw_query_database command. Retrieve the latest taxonomic classifications (incluidng the complete lineage from kingdom to strain) from the GTDB database using the cw_get_gtdb_taxs command. Retrieve the latest taxonomic classifications (including the complete lineage from kingdom to strain) using the cw_get_ncbi_taxs command. To protein structure files from PDB use the cw_get_pdb_structures command. To extract GenBank and/or UniProt protein sequences from a local CAZyme database, use the cw_extract_db_seqs command. To retrieve the latest taxonomic classifications from NCBI Taxonomy using the cw_get_ncbi_taxs command. To retrieve protein sequences from GenBank use the cw_get_genbank_seqs command. To retrieve protein data from UniProt, use the cw_get_uniprot_data command. To retrieve data from CAZy and compile and SQLite database using cazy_webscraper command. Command summary īelow are the list of commands (excluding required and optional arguments) included in cazy_webscraper. NCBI is queried to identify the currect source organismįor a given protein, when multiple source organisms are retrieved from CAZy for a single protein.įor more information please see the NCBI Entrez documentation. The user email address is a requirement of NCBI. Citations: cite cazy_webscraper and dependencies.Integrate a local CAZyme database into into downstream analyses.Tutorial on interrogating the data using the API.Tutorials on configuring cazy_webscraper to retrieve GTDB taxonomic classifications.Retrieving GTDB Taxonomic Classifications.Tutorials on configuring cazy_webscraper to retrieve NCBI genomic assembly data.Retrieving genomic assembly data from NCBI Assembly.Tutorials on configuring cazy_webscraper to retrieve NCBI taxonomic classifications.Retrieving NCBI Taxonomic Classifications.Tutorials on configuring cazy_webscraper to retrieve data from PDB.Tutorials on configuring the extraction of protein sequences.Extract protein squences from the local database.Retrieving Sequences from GenBank Tutorial.Retrieving Protein Sequences from GenBank. ![]() Tutorials on configuring cazy_webscraper to retrieve data from UniProt.Tutorials on configuring cazy_webscraper to scrape CAZy.
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