cazy_webscraper

cazy_webscraper is an application and Python3 package for the automated retrieval of protein data from the CAZy database. The code is distributed under the MIT license. The full documentation can be found at Read the Docs.

For full details see our publication in Microbial Genomics, which includes example analyses.

Hobbs, E. E. M, Gloster, T. M., Pritchard, L. (2023) cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets, Microbial Genomics, 9(8). https://doi.org/10.1099/mgen.0.001086

cazy_webscraper retrieves protein data from the CAZy database and stores the data in a local SQLite3 database. This enables users to integrate the dataset into analytical pipelines, and interrogate the data in a manner unachievable through the CAZy website.

Data can be retrieved for user defined datasets of interest. cazy_webscraper can recover specified CAZy Classes and/or CAZy families. These queries can be filtered by taxonomy at Kingdoms, genus, species or strain level. Successive CAZy queries can be collated into a single local database. A log of each query is recorded in the database for transparency, reproducibility and shareablity.

Using the expand subcommand, a user can expand the core dataset. Specifically, cazy_webscraper can be used to retrieve data from the following external databases for CAZymes in the local CAZyme database that meet user specified criteria, and adds the downloaded data to the local CAZyme database:

GenBank:

Protein sequences
Latest taxonomic classification - including complete lineage (including phylum, class, order and family) (version >=2.1.2)
Latest genomic assembly data (GenBank and RefSeq (when available) version accession and ID numbers) (version >=2.1.3)

UniProt:

UniProt ID/accession
Protein name
EC numbers
PDB accessions
Protein sequence (and date sequence was last updated)
Taxonomic classification (genus and species)

Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB):

Protein structure files
Structure files are written to disk, not stored in the local CAZyme database

Genome Taxonomy Database (GTDB): Retrieve the latest archaeal and bacterial taxonomic classifications (including complete lineages from kingdom to species) - available in cazy_webscraper verion >= 2.2.0.

cazy_webscraper faciltates extracting information from the local CAZyme database.

Protein sequences (retrieved from GenBank and/or UniProt) from the local CAZyme database for CAZymes matching the user specified criteria, and write to:

A single multisequence FASTA file
A FASTA file per extracted protein sequence
A local BLASTP database

The cazy_webscraper API facilitates interoggating the local CAZyme database.

Please see the full documentation at ReadTheDocs.

Updates

New in version 2.3.0

Downloading protein data from UniProt is several magnitudes faster than before - and should have fewer issues with using older version of bioservices
- Uses bioservices mapping to map directly from NCBI protein version accession to UniProt
- cw_get_uniprot_data not longer calls to NCBI and thus no longer requires an email address as a positional argument
Updated database schema: Changed Genbanks 1--* Uniprots to Genbanks *--1 Uniprots. Uniprots.uniprot_id is now listed in the Genbanks table, instead of listing Genbanks.genbank_id in the Uniprots table
Retrieve taxonomic classifications from UniProt
- Use the --taxonomy/-t flag to retrieve the scientific name (genus and species) for proteins of interest
- Adds downloaded taxonomic information to the UniprotsTaxs table
Improved clarrification of deleting old records when using cw_get_uniprot_data
- Separate arguments to delete Genbanks-EC number and Genbanks-PDB accession relationships that are no longer listed in UniProt for those proteins in the local CAZyme database for proteins whom data is downloaded from UniProt
- New args:
  - --delete_old_ec_relationships = deletes Genbank(protein)-EC number relationships no longer in UniProt
  - --delete_old_ecs = deletes EC numbers in the local db not linked to any proteins
  - --delete_old_pdb_relationships = deletes Genbank(protein)-PDB relationships no longer in UniProt
  - --delete_old_pdbs = deletes PDB accessions in the local db not linked to any proteins
Retrieve the local db schema
- New command cw_get_db_schema added.
- Retrieves the SQLite schema of a local CAZyme database and prints it to the terminal
Added option to skip retrieving the latest taxonomic classifications NCBI taxonomies
- By default, when retreiving data from CAZy, cazy_webscraper retrieves the latest taxonomic classifications for proteins listed under multiple tax
- To increase scrapping time, and to reduce burden on the NCBI-Entrez server, if this data is not needed (e.g. GTDB taxs will be use) this step can be skipped by using the new --skip_ncbi_tax flag.
- When skipping retrieval of the latest taxa classifications from NCBI, cazy_webscraper will add the first taxa retrieved from CAZy for those proteins listed under mutliple taxa

Documentation

The full documentation can be found at Read the Docs.

Our paper: Implementation and demonstration of use

For a full description of the operation and examples of use, please see our paper in (BioRxiv)[https://www.biorxiv.org/content/10.1101/2022.12.02.518825v1.full].

Hobbs, E. E. M., Gloster, T. M., and Pritchard, L. (2022) ‘cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets’, bioRxiv, https://doi.org/10.1101/2022.12.02.518825

Database structure

You can view the database schema here and find a PDF of the database schema here.

Contributions

We welcome contributions and suggestions. You can raise issues at this repository, or fork the repository and submit pull requests, at the links below:

cazy_webscraper
Citation
Best practice
Documentation
Creating a local CAZyme database
- Combining configuration filters
- Default CAZy class synonyms
Retrieve data from UniProt
- Configuring UniProt data retrieval
Retrieving protein sequences from GenBank
- Configuring GenBank protein sequence data retrieval
Extracting protein sequences from the local CAZyme database and building a BLAST database
- Configuring extracting sequences from a local CAZyme db
Retrieving protein structure files from PDB
- Configuring PDB protein structure file retrieval
Retrieving NCBI taxonomies
- Configuring retrieving NCBI taxonomies
Retrieving genomic assembly data from NCBI
- Configuring retrieving genomic assembly data
Retrieving GTDB taxonomies
- Configuring retrieving GTDB taxonomies
The cazy_webscraper API or Interrogating the local CAZyme database
Configuring cazy_webscraper using a YAML file
CAZy coverage of GenBank
- Configure calculating CAZy coverage of GenBank
Integrating a local CAZyme database
Database schema
Contributions
License and copyright

Features in the pipeline:

Retrieve and stored PubMed IDs in the local CAZyme database
Fix any remaining bugs we can find (if you find a bug, please report it and provide as detailed bug report as possible!)
Increase unit test coverage
Automate analysing the taxonomic distribution across CAZy and datasets of interest, including generating a final report

Citation

If you use cazy_webscraper, please cite the following publication:

Hobbs, E. E. M, Gloster, T. M., Pritchard, L. (2023) cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets, Microbial Genomics, 9(8). https://doi.org/10.1099/mgen.0.001086

The supplementary information for this manuscript is available via the BioRxiv server, and in the manuscript directory in this repository.

cazy_webscraper depends on a number of tools. To recognise the contributions that the authors and developers have made, please also cite the following:

When making an SQLite database:

Hipp, R. D. (2020) SQLite, available: https://www.sqlite.org/index.html.

Retrieving taxonomic, genomic or sequence data from NCBI:

Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, 25(11), 1422-1423. Wheeler,D.L., Benson,D.A., Bryant,S., Canese,K., Church,D.M., Edgar,R., Federhen,S., Helmberg,W., Kenton,D., Khovayko,O. et al (2005) Database resources of the National Centre for Biotechnology Information: Update, Nucleic Acid Research, 33, D39-D45

Retrieving data from UniProt:

Cokelaer, T., Pultz, D., Harder, L. M., Serra-Musach, J., Saez-Rodriguez, J. (2013) BioServices: a common Python package to access biological Web Services programmatically, Bioinformatics, 19(24), 3241-3242.

Downloading protein structure files from RSCB PDB:

Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., et al (2022) The Protein Data Bank, Nucleic Acids Research, 28(1), 235-242. Hamelryck, T., Manderick, B. (2003), PDB parser and structure class implemented in Python. Bioinformatics, 19 (17), 2308–2310

Retrieving and using taxonomic data from GTDB:

Parks, D.H., Chuvochina, M., Rinke, C., Mussig, A.J., Chaumeil, P., Hugenholtz, P. (2022) GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Research, 50(D1), D785-D794.

Best practice

When performing a series of many automated calls to a server it is best to do this when traffic is lowest, such as at weekends or overnight at the server.

Documentation

Please see the full documentation at ReadTheDocs.

Installation

cazy_webscraper can be installed via conda or pip:

conda install -c bioconda cazy_webscraper

Please see the conda documentation and bioconda documentation for further details.

pip install cazy_webscraper

Please see the pip documentation for further details.

Quickstart

We have produced a “Getting Started With cazy_webscraper” poster.

To download all of CAZy and save the database in the default location (the cwd) with the default name (cazy_webscraper_<date>_<time>.db) use the following command:

cazy_webscraper <user_email>

Version and citation

To retrieve the version, use the following command:

cazy_webscraper -V

cazy_webscraper --version

To retrieve the citation to use:

cazy_webscraper -C

cazy_webscraper --citation

Command summary

Below are the list of commands (excluding required and optional arguments) included in cazy_webscraper.

CAZy

To retrieve data from CAZy and compile and SQLite database using cazy_webscraper command.

UniProt

To retrieve protein data from UniProt, use the cw_get_uniprot_data command.

The following data can be retrieved:

UniProt accession
Protein name
EC numbers
PDB accession
Protein sequences

GenBank

To retrieve protein sequences from GenBank use the cw_get_genbank_seqs command.

Extract sequences

To extract GenBank and/or UniProt protein sequences from a local CAZyme database, use the cw_extract_db_seqs command.

PDB

To protein structure files from PDB use the cw_get_pdb_structures command.

Note: PDB structure files are retrieved for the PDB accessions that are in a local CAZyme database created using cazy_webscraper. A freshly built CAZyme database only contains NCBI protein accessions, taxonomic kingdoms, source organisms, and CAZy family annotations. Therefore, the cw_get_uniprot_data command must be used to retrieve PDB accessions from the UniProt database prior to using the cw_get_pdb_structures command.

Interrogate the database

To interrogate the database, use the cw_query_database command.

Local CAZyme database schema

The schema of a local CAZyme database can be retrieved using cazy_webscraper:

cw_get_db_schema <path to local CAZyme database>

Alternatively, sqlite3 can be used to retrieve the schema:

sqlite3 <path to local CAZyme database> .schema

A visual representation of the db schema when using cazy_webscraper version >= 2.3.0 can be found here.

Creating a local CAZyme database

Command line options for cazy_webscraper, which is used to scrape CAZy and compile a local SQLite database. Options are written in alphabetical order.

email - [REQUIRED] User email address. This is required by NCBI Entrez for querying the Entrez server. Email address is not required when printing out the citation and version number information

--cache_dir - Path to cache dir to be used instead of default cache dir path.

--cazy_data - Path to a txt file downloaded from CAZy containing a CAZy db data dump.

--cazy_synonyms - Path to a JSON file containing accepted CAZy class synonsyms if the default are not sufficient.

--classes - list of classes from which all families are to be scrape.

--config, -c - Path to a configuration YAML file. Default: None.

--citation, -C - Print the cazy_webscraper citation. When called, the program terminates after printng the citation and CAZy is not scraped.

--db_output, -o - Path to write out a new local CAZyme database.

--database, -d - Path to an existings local CAZyme database to add newly scraped too. Default: None.

Do not use --db_output and --database at the same time.

If --db_output and --database are not called, cazy_webscraper writes out a local CAZyme database to the cwd with the standardised name cazy_webscraper_<date>_<time>.db

--delete_old_relationships - Detele old CAZy family annotations of GenBank accessions. These are CAZy family annotations of a given GenBank accession are in the local database but the accession is not longer associated with those CAZy families, so delete old accession-family relationships.

--families - List of CAZy (sub)families to scrape.

--force, -f - force overwriting existing output file. Default: False.

--genera - List of genera to restrict the scrape to. Default: None, filter not applied to scrape.

--kingdoms - List of taxonomic kingdoms to restrict the scrape to. Default: None, filter is not applied.

--log, -l - Target path to write out a log file. If not called, no log file is written. Default: None (no log file is written out).

--nodelete, -n - When called content in an existing output directory is not deleted.

_When the --db_output flag is used, cazy_webscraper will create any necessary parent directories. If the direct/immediate parent directory of the database exists, by default cazy_webscraper will delete the content in this parent directory.

--ncbi_batch_size - The number of protein IDs submitted per batch to NCBI, when retrieving taxonomic classifications. Default 200.

--nodelete_cache - When called, content in the existing cache dir will not be deleted. Default: False (existing content is deleted).

--nodelete_log - When called, content in the existing log dir will not be deleted. Default: False (existing content is deleted).

--retries, -r - Define the number of times to retry making a connection to CAZy if the connection should fail. Default: 10.

--skip-ncbi_tax - Skip retrieving the latest taxonomic information for NCBI were multiple taxonomic classifications are retrieved from CAZy for a protein. The first taxonomy retrieved from CAZy will be added to the local CAZyme database. Default False - the first taxon listed for each protein is added to the local CAZyme database.

--sql_echo - Set SQLite engine echo parameter to True, causing SQLite to print log messages. Default: False.

--subfamilies, -s - Enable retrival of CAZy subfamilies, otherwise only CAZy family annotations will be retrieved. Default: False.

--species - List of species written as Genus Species) to restrict the scraping of CAZymes to. CAZymes will be retrieved for all strains of each given species.

--strains - List of specific species strains to restrict the scraping of CAZymes to.

--timeout, -t - Connection timout limit (seconds). Default: 45.

--validate, - Retrieve CAZy family population sizes from the CAZy website and check against the number of family members added to the local CAZyme database, as a method for validating the complete retrieval of CAZy data.

--verbose, -v - Enable verbose logging. This does not set the SQLite engine echo parameter to True. Default: False.

--version, -V - Print cazy_webscraper version number. When called and the version number is printed, cazy_webscraper is immediately terminated.

Combining configuration filters

cazy_webscraper applies filters in a successive and layered structure.

CAZy class and family filters are applied first.

Kingdom filters are applied second.

Lastly, taxonomy (genus, species and strain) filters are applied.

Default CAZy class synonyms

CAZy classes are accepted in the written long form (such as Glycoside Hydrolases) and in their abbreviated form (e.g. GH).

Both the plural and singular abbreviated form of a CAZy class name is accepted, e.g. GH and GHs.

Spaces, hythens, underscores and no space or extract character can be used in the CAZy class names. Therefore, Glycoside Hydrolases, Glycoside-Hydrolases, Glycoside_Hydrolases and GlycosideHydrolases are all accepted.

Class names can be written in all upper case, all lower case, or mixed case, such as GLYCOSIDE-HYDROLASES, glycoside hydrolases and Glycoside Hydrolases. All lower or all upper case CAZy class name abbreviations (such as GH and gh) are accepted.

Retrieve data from UniProt

[UniProtKB] is one of the largest protein database, incorporating data from the [PDB] structure database, NCBI and other protein annotation databases.

cazy_webscraper can retrieve protein data from UniProt for proteins catalogued in a local CAZyme database created using cazy_webscraper. Specifically, for each protein, cazy_webscraper can retrieve:

The UniProt accession
Protein name
PDB accessions of associated structure files from the PDB database
EC number annnotations
Protein sequence from the UniProt

cazy_webscraper always retrieves the UniProt accession and protein name, but the retrieval of PDB accession, EC numbers and protein sequences is optional.

Data can be retrieived for all proteins in the local CAZyme database, or a specific subset. CAZy class, CAZy family, genus, species, strains, kingdom and EC number filters can be defined in order to define a dataset to retrieve protein data for.

To retrieve all UniProt data for all proteins in a local CAZyme datbase, using the following command:

cw_get_uniprot_data <path_to_local_CAZyme_db> --ec --pdb --sequence

Configuring UniProt data retrieval

Below are listed the command-line flags for configuring the retrieval of UniProt data.

database - [REQUIRED] Path to a local CAZyme database to add UniProt data to.

--bioservices_batch_size - Change the query batch size submitted via bioservices to UniProt to retrieve protein data. Default is 1000. See the UniProt REST API documentation for batch size limits.

--cache_dir - Path to cache dir to be used instead of default cache dir path.

--cazy_synonyms - Path to a JSON file containing accepted CAZy class synonsyms if the default are not sufficient.

--classes - List of classes to retrieve UniProt data for.

--config, -c - Path to a configuration YAML file. Default: None.

--ec, -e - Enable retrieval of EC number annotations from UniProt

--ec_filter - Limist retrieval of protein data to proteins annotated with a provided list of EC numbers. Separate the EC numbers bu single commas without spaces. Recommend to wrap the entire str in quotation marks, for example:

cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'

--families - List of CAZy (sub)families to scrape.

--force - Force writing in existing cache directory.

--genbank_accessions - Path to text file containing a list of GenBank accessions to retrieve protein data for. A unique accession per line.

--genera - List of genera to restrict the scrape to. Default: None, filter not applied to scrape.

--kingdoms - List of taxonomic kingdoms to restrict the scrape to. Default: None, filter is not applied.

--log, -l - Target path to write out a log file. If not called, no log file is written. Default: None (no log file is written out).

--name_update - Boolean, whether to overwrite the existing protein name (previously retrieved from UniProt). Default: do not update.

--nodelete_cache - When called, content in the existing cache dir will not be deleted. Default: False (existing content is deleted).

--nodelete_log - When called, content in the existing log dir will not be deleted. Default: False (existing content is deleted).

--pdb, -p - Enable retrieval of PDB accessions. Default, PDB accessions not retrieved.

--retries, -r - Define the number of times to retry making a connection to CAZy if the connection should fail. Default: 10.

--delete_old_ec_relationships - Boolean, delete old Genbanks-EC number relationships - For those proteins in the local db for whom data is downloaded from UniProt, compare the current links between the proteins in the Genbanks table and EC numbers in the Ecs table. Delete Genbanks-Ecs relationships that are not longer listed in the respective protein records in UniProt.

--delete_old_ecs - Boolean, delete EC number - Delete EC numbers that are not linked to any proteins listed in the Genbanks table. These can arise from multiple retrievals of data from the UniProt data over a period of time during UniProt records have been updated.

--delete_old_pdb_relationships - Boolean, delete old Genbanks-PDB relationships - For those proteins in the local db for whom data is downloaded from UniProt, compare the current links between the proteins in the Genbanks table and PDB accessions in the Pdbs table. Delete Genbanks-Pdbs relationships that are not longer listed in the respective protein records in UniProt.

--delete_old_pdbs - Boolean, delete PDB accessions - Protein relationships that are no longer listed in UniProt, i.e. an PDB accessions that are no longer included in UniProt but is in the local database. If set to TRUE these relationships will be DELETED from the database.

--use_uniprot_cache - Path to a JSON file, keyed by UniProt accessions/IDs and valued by dicts containing {'gbk_acc': str, 'db_id': int}. This file part of the cache created by cw_get_uniprot_data. This is option to skip retrieving the UniProt IDs for a set of GenBank accessions, if retrieving data for the same dataset (this save a lot of time!)

skip_download - Bool, default False. If set to True, only uses data from UniProt cache and will not download new data from UniProt.

--sequence, -s - Retrieve protein amino acid sequences from UniProt

--sql_echo - Set SQLite engine echo parameter to True, causing SQLite to print log messages. Default: False.

--species - List of species written as Genus Species) to restrict the scraping of CAZymes to. CAZymes will be retrieved for all strains of each given species.

--strains - List of specific species strains to restrict the scraping of CAZymes to.

--taxonomy, -t - Retrieve taxonomic classifications (genus species) and add to the local CAZyme database

--timeout - Connection timout limit (seconds). Default: 45.

--update_name - If a newer version of the protein name is available, overwrite the existing name for the protein in the database. Default is false, the protein name is not overwritten and updated.

--update_seq - If a newer version of the protein sequence is available, overwrite the existing sequence for the protein in the database. Default is false, the protein sequence is not overwritten and updated.

--use_uniprot_cache - Path to JSON file containing data previosuly retrieved from UniProt by cazy_webscraper, use if an error occurred while adding the data to the local CAZyme database. This will skip the retrieval of data from UniProt, and the cached data will be added to the local CAZyme database. This can also be shared with others to add the same data to their local CAZyme database.

--uniprot_batch_size - Size of an individual batch query submitted to the UniProt REST API to retrieve the UniProt accessions of proteins identified by the GenBank accession. Default is 150. The UniProt API documentation recommands batch sizes of less than 20,000 but batch sizes of 1,000 often result in HTTP 400 errors. It is recommend to keep batch sizes less than 1,000, and ideally less than 200.

--verbose, -v - Enable verbose logging. This does not set the SQLite engine echo parameter to True. Default: False.

UniProt batch sizes: Note that according to Uniprot (June 2022), there are various limits on ID Mapping Job Submission:

========= ===================================================================================== Limit Details ========= ===================================================================================== 100,000 Total number of ids allowed in comma separated param ids in /idmapping/run api 500,000 Total number of “mapped to” ids allowed 100,000 Total number of “mapped to” ids allowed to be enriched by UniProt data 10,000 Total number of “mapped to” ids allowed with filtering ========= =====================================================================================

UniProt data retrieval cache

The tables retrieved from UniProt are converted to dataframes, and written out as CSV files in the cache directory
The parsed UniProt data as a single JSON file

Retrieveing protein seqences from GenBank

Protein amino acid sequences can be retrieved for proteins in a local CAZyme database using cazy_webscraper. Protein sequences can be retrieved for a specific subset of proteins, identified through the use of CAZy class, CAZy family, taxonomy (kingdom, genus, species and strain) filters, and EC number filters. The retrieved protein sequences are written to the local CAZyme database.

Extracting protein sequences from the local CAZyme database and writing them to a BLAST database and/or FASTA file(s) is covered in the next section.

To retrieve all GenBank protein seuqneces for all proteins in a local CAZyme datbase, using the following command:

cw_get_genbank_seqs <path_to_local_CAZyme_db>

Configuring GenBank protein sequence retrieval

Below are listed the command-line flags for configuring the retrieval of protein sequences from GenBank.

database - [REQUIRED] Path to a local CAZyme database to add UniProt data to.

email - [REQUIRED] User email address, required by NCBI Entrez.

--batch_size - Size of batch query posted to NCBI Entrez. Default 150.

--cache_dir - Path to cache dir to be used instead of default cache dir path.

--cazy_synonyms - Path to a JSON file containing accepted CAZy class synonsyms if the default are not sufficient.

--config, -c - Path to a configuration YAML file. Default: None.

--classes - List of classes from which all families are to be scrape.

cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'

--force, -f - Force writing cachce to exiting cache directory.

--families - List of CAZy (sub)families to scrape.#

--kingdoms - List of taxonomy kingdoms to retrieve UniProt data for.

--genbank_accessions - Path to text file containing a list of GenBank accessions to retrieve protein data for. A unique accession per line.

--genera - List of genera to restrict the scrape to. Default: None, filter not applied to scrape.

--log, -l - Target path to write out a log file. If not called, no log file is written. Default: None (no log file is written out).

--nodelete_cache - When called, content in the existing cache dir will not be deleted. Default: False (existing content is deleted).

--retries, -r - Define the number of times to retry making a connection to CAZy if the connection should fail. Default: 10.

--seq_dict, - Path to a JSON file, keyed by GenBank accessions and valued by protein sequence. This file is created as part of the cache, after all protein sequences are retrieved from GenBank.

--seq_update - If a newer version of the protein sequence is available, overwrite the existing sequence for the protein in the database. Default is false, the protein sequence is not overwritten and updated. This skips the retrieval of the protein sequences from GenBank.

--sql_echo - Set SQLite engine echo parameter to True, causing SQLite to print log messages. Default: False.

--species - List of species written as Genus Species) to restrict the scraping of CAZymes to. CAZymes will be retrieved for all strains of each given species.

--strains - List of specific species strains to restrict the scraping of CAZymes to.

--verbose, -v - Enable verbose logging. This does not set the SQLite engine echo parameter to True. Default: False.

GenBank sequence retrieval cache

cazy_webscraper produces three cache files, which are written to the cache dir:

no_seq_retrieved.txt which lists the GenBank accessions for which no sequence could be retrieved from GenBank
seq_retrieved.txt which list GenBank accessiosn for which a sequence was retrieved from GenBank
JSON file keyed by GenBank accessions and valued by the retrieved protein sequence

Extracting protein sequences from the local CAZyme database and building a BLAST database

Protein sequences from GenBank and UniProt that are stored in the local CAZyme database can be extracted using cazy_webscraper, and written to any combination of:

1 FASTA file per unique protein
A single FASTA file containing all extracted seqences
A BLAST database

FASTA file format: Protein sequences extracted from a local CAZyme database are written out with the GenBank/UniProt accession as the protein ID, and the name of the source database (‘GenBank’ or ‘UniProt’) as the description.

To extract all protein seqeunces from the local CAZyme database using the following command structure:

cw_extract_db_seqs <path_to_local_CAZyme_db> genbank uniprot

To retrieve protein sequences from GenBank or UniProt, name only the respective database. For example, to retrieve only GenBank proteins:

cw_extract_db_seqs <path_to_local_CAZyme_db> genbank

Configuring extracting sequences from a local CAZyme db

Below are listed the command-line flags for configuring the extraction of protein sequences from the local CAZyme db.

database - [REQUIRED] Path to a local CAZyme database to add UniProt data to.

source - [REQUIRED] Define source databases of protein sequences. Accepts ‘genbank’ and ‘uniprot’. To list both, separate with a single space (‘ ‘)

cw_extract_sequence cazy_database.db genbank uniprot

The database names are not case sensitive, therefore, both GenBank and genbank are accepted.

-b, --blastdb - Create BLAST database of extracted protein sequences. Provide the path to the directory to store the BLAST database in.

--fasta_dir - Write out each extracted sequence to a separate FASTA file in the provided dir. Provide a path to a directory to write out the FASTA files.

--fasta_file - Write out all extracted sequences to a single FASTA file. Provide a path to write out the FASTA file.

Note: at least one of --blastdb, --fasta_dir, and --fasta_file must be called to inform cazy_webscraper where to write the output to. If none are called sequences will be extracted.

--cache_dir - Path to cache dir to be used instead of default cache dir path.

--cazy_synonyms - Path to a JSON file containing accepted CAZy class synonsyms if the default are not sufficient.

--config, -c - Path to a configuration YAML file. Default: None.

--classes - List of classes from which all families are to be scrape.

cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'

--force, -f - Force overwriting exsiting files and writing to existing output directory.

--families - List of CAZy (sub)families to scrape.#

--kingdoms - List of taxonomy kingdoms to retrieve UniProt data for.

--genbank_accessions - Path to text file containing a list of GenBank accessions to retrieve protein data for. A unique accession per line.

--genera - List of genera to restrict the scrape to. Default: None, filter not applied to scrape.

--log, -l - Target path to write out a log file. If not called, no log file is written. Default: None (no log file is written out).

--nodelete - When called, content in the existing output dir will not be deleted. Default: False (existing content is deleted).

--nodelete_cache - When called, content in the existing cache dir will not be deleted. Default: False (existing content is deleted).

--sql_echo - Set SQLite engine echo parameter to True, causing SQLite to print log messages. Default: False.

--species - List of species written as Genus Species) to restrict the scraping of CAZymes to. CAZymes will be retrieved for all strains of each given species.

--strains - List of specific species strains to restrict the scraping of CAZymes to.

--uniprot_accessions - Path to text file containing a list of UniProt accessions to retrieve protein data for. A unique accession per line.

--verbose, -v - Enable verbose logging. This does not set the SQLite engine echo parameter to True. Default: False.

Retrieving protein structure files from PDB

cazy_webscraper can retrieve protein structure files for proteins catalogued in a local CAZyme database. Structure files can be retrieved for all proteins in the database or a subset of proteins, chosen by defining CAZy class, CAZy family, taxonomy (kingdom, genus, species and strain) filters, and EC number filters.

Retrieval of structure files from PDB is performed by the BioPython module PDB [Cock et al., 2009], which writes the downloaded structure files to the local disk. Therefore, the downloaded structure files are not stored in the local CAZyme database at the present.

Cock, P. J. A, Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A. et al. (2009) ‘Biopython: freely available Python tools for computaitonal molecular biology and bioinformatics’, Bioinformatics, 25(11), pp. 1422-3.

To retrieve structure files for all proteins in a local CAZyme database in mmCif and pdb format, use the following command:

cw_get_pdb_structures <path_to_local_CAZyme_db> mmcif,pdb

Protein structure files can be retrieved in a variety of formats, including:

mmCif (default, PDBx/mmCif file),
pdb (format PDB),
xml (PDBML/XML format),
mmtf (highly compressed),
bundle (PDB formatted archive for large structure}

Configuring PDB protein structure file retrieval

Below are listed the command-line flags for configuring the retrieval of protein structure files from PDB.

database - [REQUIRED] Path to a local CAZyme database to add UniProt data to.

pdb [REQUIRED] The file types to be retrieved from PDB. The following file types are supported:

mmCif
pdb
xml
mmft
bundle To chose multiple file types, list all desired file types, separting the files using a single space (‘ ‘). For example:
```
cw_get_genbank_seq my_cazyme_db/cazyme_db.db mmcif pdb xml
```
Providing the file types is case sensitive, but the order the file types are listed does not matter.

--batch_size - Size of an individual batch query of PDB accessions submitted to PDB. Default is 150.

--cache_dir - Path to cache dir to be used instead of default cache dir path.

--cazy_synonyms - Path to a JSON file containing accepted CAZy class synonsyms if the default are not sufficient.

--config, -c - Path to a configuration YAML file. Default: None.

--classes - List of classes from which all families are to be scrape.

cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'

-F, --file_only - Only add seqs provided via JSON and/or FASTA file. Do not retrieved data from NCBI.

--families - List of CAZy (sub)families to scrape.

--genbank_accessions - Path to text file containing a list of GenBank accessions to retrieve protein data for. A unique accession per line.

--genera - List of genera to restrict the scrape to. Default: None, filter not applied to scrape.

--kingdoms - List of taxonomy kingdoms to retrieve UniProt data for.

--log, -l - Target path to write out a log file. If not called, no log file is written. Default: None (no log file is written out).

--nodelete - When called, content in the existing output dir will not be deleted. Default: False (existing content is deleted).

--nodelete_cache - When called, content in the existing cache dir will not be deleted. Default: False (existing content is deleted).

--outdir, -o - Output directory to write out downloaded protein structure files to. Default is to write out the downloaded structure files to the current working directory.

--overwrite - Overwrite existing structure files with the same PDB accession as files being downloaded. Default false, do not overwrite existing files.

--retries, -r - Define the number of times to retry making a connection to CAZy if the connection should fail. Default: 10.

--seq_dict - Path to a JSON file, keyed by GenBank accessions and valued by protein sequence. Add seqs in file to the local CAZyme database.

--seq_file - Path to a FASTA file, keyed by GenBank accessions and valued by protein sequence. Add seqs in file to the local CAZyme database.

--sql_echo - Set SQLite engine echo parameter to True, causing SQLite to print log messages. Default: False.

--species - List of species written as Genus Species) to restrict the scraping of CAZymes to. CAZymes will be retrieved for all strains of each given species.

--strains - List of specific species strains to restrict the scraping of CAZymes to.

--timeout, -t - Connection timout limit (seconds). Default: 45.

--uniprot_accessions - Path to text file containing a list of UniProt accessions to retrieve protein data for. A unique accession per line.

--verbose, -v - Enable verbose logging. This does not set the SQLite engine echo parameter to True. Default: False.

Retrieving NCBI taxonomies

Taxonomic opinions frequently change, and CAZy can fall out of sync with the latest taxonomic classifications with NCBI. To maintain an updated CAZyme database, cazy_webscraper can be used to retrieve the latest taxonomic classifications from NCBI for CAZymes in a local CAZyme database that meet the user’s specified criteria. The downloaded taxonomic data is added to the local CAZyme database.

The complete lineage data is retrieved from NCBI. Whereas CAZy lists only the kingdom, genus, species and strain, cazy_webscraper retrieves the full taxonomic lineage from NCBI and stores the complete lineage in the NcbiTaxs table in the local CAZyme database. This include:

Kingdom
Phylum
Class (stored as tax_class in the local CAZyme database due to keyword classes in Python)
Order(stored as tax_order in the local CAZyme database due to keyword classes in SQL)
Family
Genus
Species
Strain

The command for retrieving the latest taxonomic classifications from the NCBI Taxonomy database using cazy_webscraper is cw_get_ncbi_taxs.

Configuring retrieving NCBI taxonomies

Below are listed the command-line flags for configuring the retrieval of taxonomic classifications from the NCBI Taxonomy database, and adding them to the local CAZyme database.

database - [REQUIRED] Path to a local CAZyme database to add UniProt data to.

email - [REQUIRED] User email address (required by Entrez)

--batch_size - Size of an individual batch query of NCBI sequence version accessions to NCBI. Default is 150.

--cache_dir - Path to cache dir to be used instead of default cache dir path.

--cazy_synonyms - Path to a JSON file containing accepted CAZy class synonsyms if the default are not sufficient.

--config, -c - Path to a configuration YAML file. Default: None.

--classes - List of classes from which all families are to be scrape.

cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'

--families - List of CAZy (sub)families to scrape.

--force - Force writing to exiting cache directory.

--genbank_accessions - Path to text file containing a list of GenBank accessions to retrieve protein data for. A unique accession per line.

--genera - List of genera to restrict the scrape to. Default: None, filter not applied to scrape.

--kingdoms - List of taxonomy kingdoms to retrieve UniProt data for.

--log, -l - Target path to write out a log file. If not called, no log file is written. Default: None (no log file is written out).

--nodelete_cache - When called, content in the existing cache dir will not be deleted. Default: False (existing content is deleted).

--retries, -r - Define the number of times to retry making a connection to NCBI if the connection should fail. Default: 10.

--sql_echo - Set SQLite engine echo parameter to True, causing SQLite to print log messages. Default: False.

--species - List of species written as Genus Species) to restrict the scraping of CAZymes to. CAZymes will be retrieved for all strains of each given species.

--strains - List of specific species strains to restrict the scraping of CAZymes to.

--uniprot_accessions - Path to text file containing a list of UniProt accessions to retrieve protein data for. A unique accession per line.

--update_gbk - Update the existing NCBI taxonomy data in records in the Genbanks table already with NCBI taxonomy data. By default, NCBI tax data is only added to records in the Genbanks table if NCBI taxonomy data is not already presented in the record.

--update_taxs - Update existing NCBI taxonomy data in the NcbiTaxs table. By default onlt add new NCBI taxonomy data, do not update (and thus overwrite) existing data.

--use_lineage_cache - Use cached lineage data previously compliled by cazy_webscraper - skips retrieving NCBI Tax and Protein IDs and lineage data from NCBI

--use_protein_ids - Path to plain text file containing a tab delimited list of (1) NCBI Protein ID and (2) NCBI sequence version accession. Used cached NCBI Protein IDs.

--use_tax_ids - Path to plain text file listing a unique NCBI Taxonomy ID per line. Get lineages for cached NCBI Tax IDs.

--verbose, -v - Enable verbose logging. This does not set the SQLite engine echo parameter to True. Default: False.

Retrieving genomic assembly data from NCBI

CAZy does not list the source genomic assembly for proteins catalogued in its database. cazy_webscraper can be used to retrieve the latest genomic assembly data from NCBI for CAZymes in a local CAZyme database that meet the user’s specified criteria. The downloaded assembly data is added to the local CAZyme database entails:

Assembly name
GenBank genomic version accession
GenBank genomic ID
RefSeq genomic version accession
RefSeq genomic ID

The command for retrieving genomic assembly data from the NCBI Assembly database using cazy_webscraper is cw_get_genomics.

Configuring retrieving genomic assembly data

Below are listed the command-line flags for configuring the retrieval of genomic assembly data from the NCBI Assembly database, and adding the data to the local CAZyme database.

database - [REQUIRED] Path to a local CAZyme database to add UniProt data to.

email - [REQUIRED] User email address (required by Entrez)

--batch_size - Size of an individual batch query of NCBI sequence version accessions to NCBI. Default is 150.

--cache_dir - Path to cache dir to be used instead of default cache dir path.

--cazy_synonyms - Path to a JSON file containing accepted CAZy class synonsyms if the default are not sufficient.

--config, -c - Path to a configuration YAML file. Default: None.

--classes - List of classes from which all families are to be scrape.

cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'