Tutorial on interrogating the data using the API

cazy_webscraper includes an API that can be used to interrogate the data in the local CAZyme database and write out the retrieved data in JSON and/or CSV format.

By default cazy_webscraper only includes the GenBank accessions of proteins matching the provided criteria, but the inclusion of additional data (such as protein squences, UniProt accessions, EC numbers, etc) is fully customisable.

For interrogating the data and retrieving proteins matching the provided criteria, many of the same configuration options apply to the retrieval of protein data from CAZy, UniProt, GenBank and PDB.

cazy_webscraper can be configured via the command line and/or via a YAML configuration file.

This page runs through examples of how to combine the various ‘filters’ that can be applied, to fully customised the retrieval of protein data from the local CAZyme database. These tutorials are designed for those with less experience using command-line tools.

Note

If you installed cazy_webscraper using bioconda or pip to invoke cazy_webscraper to retrieve UniProt data call it using cw_query_database - this is the method used in this tutorial. If you installed cazy_webscraper from source then you will need to invoke cazy_webscraper from the root of the repo using the command python3 cazy_webscraper/api/cw_query_database.py.

From this point on, we will be discusseing the cw_query_database command, which is used by cazy_webscraper for retrieving protein data from the local CAZyme database. We also presume you are comfortable configuring cazy_webscraper for the scraping of data from CAZy.

Configuration via the command line

cw_query_database requires two arguments: * The path to the local CAZyme database created using cazy_webscraper * The file formats to write out the output

Therefore, cw_query_database can be enabled using a simple command structure:

cazy_webscraper <path to the local CAZyme db> <file formats>

For example, if our database was stored in cazy/cazyme.db and we want to write the output to a csv file, we would used:

cazy_webscraper cazy/cazyme.db csv

Note

Make sure cw_query_database is pointed directly at the database file.

When no optional arguments are provided, the default behaviour is invoked. The default behaviour is to: retrieve only the GenBank accessions of all CAZymes in the local CAZyme CAZyme db

Accepted file formats

cw_query_database can write the output to a csv or json file.

These are provided as the second arguments to cw_query_database. To write out both a csv and json file use both csv and json after the path to the local CAZyme database, separted with a single space.

cw_query_database <path to local CAZyme db> csv json

Note

The order csv and json are written does not matter.

Warning

Both csv and json are case sensitive.

Options configurable at the command line

The following behaviours of the cw_query_database can be configured at the command-line in the terminal:

  • Limit the retrieval of protein data to CAZymes in the local databaes from specific CAZy classes, CAZy families, kingdoms, genuera, species, strains and/or EC numbers

  • Including any combination of the following in the output, along side the GenBank accessions:

    • CAZy class

    • CAZy family

    • CAZy subfamily

    • Kingdom

    • Genus

    • Scientific name of the source organsim

    • Protein sequence retrieved from GenBank

    • UniProt accession

    • Protein name retrieved from UniProt

    • EC numbers

    • PDB accessions

    • Protein sequence retrieved from UniProt

  • Write the output in JSON and/or CSV format

  • Choose an output directory

  • Force overwriting existing files

  • Enable verbose logging during the operation of the webscraper

Here you can find a full list of the command-line flags and options.

Choosing an output directory

By default, cw_query_database writes all output files to the current working directory.

To specify an alternative output directory, using the --output_dir/-o flag, followed by the path to the target output directory. cw_query_database will build all necessary parent and child output directories.

For example, to write the output to the directory my_cazy_data use the following command:

If the output directory already exists, cw_query_database will raise an error warning the output directory already exists and close. This is to prevent accidently writing data to the wrong location.

To force cw_query_database to write the data to an existing output directory, add the --force/-f flag.

By default cw_query_database will delete all content already present in the existing output directory. To retain the data in the existing output directory, add the --nodelete/-n flag.

Note

The --force and --nodelete flags are only applied when the --output_dir flag is used. cw_query_database will not delete content in the current working directory when writing to the current working directory when the --output_dir flag is not used.

Overwrite existing files

cw_query_database automatically compiles the names of the output files.

The file names of all output files are composed of the name of the local CAZyme database, followed by the names of the data retrieved from the local CAZyme database. For example, retrieving the following data from the local CAZyme database called cazy_database.db: * CAZy family annotation * CAZy subfamily annotations * EC numbers * PDB accessions Will produce the following file name: cazy_database_gbkAcc_fams_subfams_ec_pdb.

Note

_gbkAcc is always included in the file name because GenBank accessions are always retrieved and written to the output by cw_query_database.

Both the json and csv files are given the same name, the files only differ in their file extension.

An optional prefix can be applied to all output file names using the -p/--prefix flag, followed by the desired prefix. For example, using the same example as above, the prefix ‘engineering_candidates_` can be applied to every output file by adding the following to command:

This will produce output files with the file name engineering_candidates_cazy_database_fams_subfams_ec_pdb.

If files matching the file names compiled by cw_query_database already existing at the target output location, cw_query_database will raise a warning that output files already existing and terminate. This is to prevent accidently overwriting data files.

To overwrite existing datafiles add the --overwrite flag to the command. For example, the following command will retrieve all GenBank accessions stored in the local CAZyme database located at cazy/cazyme.db and write out the GenBank accessions to a file called all_gbk_acc_cazyme_gbkAcc.csv to my_cazy_data, and will not delete content in the existing output directory and will overwrite the existing output file my_cazy_data/all_gbk_acc_cazyme_gbkAcc.csv.

Retrieving protein data for CAZy classes and families to scrape

The --classes and --families flags from scraping data from CAZy are applied in the extact same way for retrieving protein data from the local CAZyme databases.

For instance, if instead of retrieving protein data for all CAZymes in your local CAZyme database, you want to retrieve protein data for CAZymes in specific CAZy classes then add the --classes flag followed by the classes you want to retrieve protein data for.

Tip

To list multiple classes, separate the classes with a single comma.

For example, if you want to retrieve protein data for all CAZymes from Glycoside Hydrolase and Carbohydrate Esterases, and write the data to a csv file, then use the command:

cw_query_database cazy/cazyme.db csv --classes GH,CE

OR

cw_query_database cazy/cazyme.db csv --classes Glycoside Hydrolases,Carbohydrate Esterases

Retrieving protein data for proteins from specific specific CAZy families is achieved using the --families flag. For example, to retrieve protein data for all proteins in PL1, PL2 and PL3 in the local CAZyme database, and write the data to csv and json files, use the following command:

cw_query_database cazy/cazyme.db json csv --families PL1,PL2,PL3

Warning

cw_query_database only accpets families written in the proper CAZy family syntax. GH1 is accepted. gh1 and GlycosideHydrolases1 are not accepted.

As with scraping data from CAZy, the --classes and --families flags can be combined. To retrieve protein data for all CAZymes in PL1, PL2, PL3 and all of GH and CE both, and write the data to a json file:

cw_query_database cazy/cazyme.db json --families PL1,PL2,PL3 --classes GH,CE

AND

cw_query_database cazy/cazyme.db json --classes GH,CE --families PL1,PL2,PL3

are accepted.

Applying taxonomic

The --kingdoms, --genera, --species and --strains flags can be used to refine the dataset of proteins to retrieve protein data by taxonomy. These flags are applied in the exact same way as they are used for the scraping of data from CAZy. Only proteins in the local CAZyme database and matching at least on of the provided taxonomy criteria will have protein data retrieved from GenBank and added to the local CAZyme datbase.

For example, if you want to retrieve protein data for all CAZymes in a local CAZyme database from bacterial and eukaryotic species then use the command

cw_query_database cazy/cazyme.db csv --kingdoms bacteria,eukaryota

Warning

The kingdoms must be spelt the same way CAZy spells them, for example use ‘eukaryot**a**’ instead of ‘eukaryot**e**’.

Note

The kingdoms are not case sensitive, therefore, both bacteria and Bacteria are accepted.

Note

You can list the kingdoms in any order. Thus, both bacteria,eukaryota and eukaryota,bacteria are accepted.

You can combine any combination of the optional flags, including combining the taxonomic filters. For example, you may wish to retrieve protein data for all CAZymes in a local CAZyme database that are derived from all viral species, Aspergillus species, Layia carnosa, Layia chrysanthemoides, Trichoderma reesei QM6a and Trichoderma reesei QM9414. To do this we would combine the respective flags for a single cw_query_database command. The command we would use would be:

cw_query_database cazy/cazyme.db csv --kingdoms viruses --genera Aspergillus --species Layia carnosa,Layia chrysanthemoides --strains Trichoderma reesei QM6a,Trichoderma reesei QM9414

Note

The order that the flags are used and the order taxa are listed does not matter, and separate multiple taxa names with a single comma with no spaces.

Warning

Use the standard scientific name formating. Captialise the first letter of genus and write a lower case letter for the first letter of the species.

Aspergillus niger is correct

asepergillus niger is incorrect

ASPERGILLUS NIGER is incorrect

Warning

When you specify a species cw_query_database will retrieval CAZymes from all strains of the species.

Applying EC number filter

The retrieval of protein data from the local CAZyme database can also be limited to proteins in a local CAZyme database that are annotated with specific EC numbers.

Having previously retrieved EC number annotations and added them to the local CAZyme database, you may wish to retrieve protein data for CAZymes annotated with specific EC numbers. To do this add the --ec_filter flag to the command, follwed by a list of EC numbers.

cw_query_database cazy/cazyme.db csv --ec_filter "EC1.2.3.4,EC2.3.4.5"

Note

Provide complete EC numbers. Both dashes (‘-’) and asterixes (‘*’) are accepted for missing digits in EC numbers.

EC1.2.3.- and EC1.2.3.* are accepted. EC1.2.3. and EC 1.2.3 are not accepted.

Note

The ‘EC’ prefix is not necessary. EC1.2.3.4 and 1.2.3.4 are accepted.

Warning

If using dashes to represent missing digits in EC numbers, it is recommended to bookend the entire EC number list in single or double quotation marks. Some terminals may misinterpret EC1.2.-.- as trying to invoke the options ‘.’

Note

cazy_webscraper will retrieve the specified UniProt data for all proteins in the local CAZyme database that are annotated with at least one of the given EC numbers. Therefore, if multiple EC numbers are given this does not mean only CAZymes will all provided EC numbers will have data retrieved from UniProt for them.

--ec_filter is based upon EC number annotations stored within the local CAZyme database. For example, if protein A is annotated with the EC1.2.3.4, but this annotation is not stored in the local CAZyme database, using --ec_filter EC1.2.3.4 will not cause cazy_webscraper to retrieve data for protein A. This is because cazy_webscraper does not know protein A is annotated with EC1.2.3.4, because this annotation is not within its database.

Warning

If --ec_filter is used along side --ec, cazy_webscraper will retrieve all EC number annotations from UniProt for all proteins in the local CAZyme database that are associated with at least one of the EC numbers provided via --ec_filter within the CAZyme database.

Combining all filters

The --classes, --families, --ec_filter, --kingdoms, --genera, --species and --strains flags can be used in any combination to define a specific subset of proteins in the local CAZyme database for whom protein data from GenBank will be retrieved.

Below we run through 3 example commands of combining these flags, writing the output to a csv file, and the resulting behaviour.

Example 1: To retrieve protein data for all CAZymes in GH, GT, CE1, CE5 and CE8, and which are derived from baceterial species we use the command:

cw_query_database cazy/cazyme.db csv --classes GH,CE --families CE1,CE5,CE8 --kingdoms bacteria

Example 2: To protein data for all CAZymes in GH and which are derived from Aspegillus and Trichoderma species we use the command:

cw_query_database cazy/cazyme.db csv -classes GH --genera Aspegillus,Trichoderma

Example 3: To retrieve protein data for all CAZymes in GH,CE and CBM which are derived from baceterial species and are annotated with at least one of EC3.2.1.23, EC3.2.1.37 and EC3.2.1.85, we use the command:

cw_query_database cazy/cazyme.db csv --ec --sequences --classes GH,CE,CBM --kingdoms bacteria --ec_filter "3.2.1.23,3.2.1.37,3.2.1.85"

Customising the output

By defauly cw_query_database only includes the GenBank accessions of the CAZymes matching the provided criteria in the final output. Any combination of the following can also be included in the output: * CAZy class * CAZy family * CAZy subfamily * Kingdom * Genus * Scientific name of the source organsim * Protein sequence retrieved from GenBank * UniProt accession * Protein name retrieved from UniProt * EC numbers * PDB accessions * Protein sequence retrieved from UniProt

To include additional data in the output use the --include flag followed by any combination (and any order) of the following options: --include - List additional data to include in the output. Multiple fields can be named, separating each with a single space (’ ‘). The accepted fields are: * ‘class’ - Include the CAZy class annotations * ‘family’ - Include the CAZy family annotations * ‘subfamily’ - Include the subfamily class annotations * ‘kingdom’ - Include the taxonomic kingdom of the source organism * ‘genus’ - Include the genus of the source organism * ‘organism’ - Include the scientific name of the source organism * ‘uniprot_acc’ - Include the UniProt accession * ‘uniprot_name’ - Include the protein name retrieved from UniProt * ‘ec’ - Include the EC number annotations * ‘pdb’ - Include the PDB accessions * ‘genbank_seq’ - Include the GenBank protein sequence * ‘uniprot_seq’ - Include the Uniprot protein sequence

Note

The quotation marks around the terms do not need to be included.

Note

No matter what additional data is included in the output, the data will be presented in the same order as presented above. For example, ‘Kingdom’ will always come before all fields listed below it. Changing the order the fields are listed in the command will not change the order data is presented in the output. For example, using --include kingdom genus organism and --include organism genus kingdom will both result in the respective columns being placed in the order of: ‘Kingdom’, ‘Genus’, ‘Organism’

To list multiple fields to include in the final output, separate each field with a singel space (’ ‘).

Example 1: To retrieve protein data for all CAZymes in GH, GT, CE1, CE5 and CE8, and which are derived from baceterial species, and include the CAZy family annotations and scientific names of the source organisms we use the command:

cw_query_database cazy/cazyme.db csv --classes GH,CE --families CE1,CE5,CE8 --kingdoms bacteria --include family organism

Example 2: To protein data for all CAZymes in GH and which are derived from Aspegillus and Trichoderma species, and include the CAZy class, EC number and PDB accessions in the output we use the command:

cw_query_database cazy/cazyme.db csv --include class ec pdb --classes GH --genera Aspegillus,Trichoderma

Example 3: To retrieve protein data for all CAZymes in GH,CE and CBM which are derived from baceterial species and are annotated with at least one of EC3.2.1.23, EC3.2.1.37 and EC3.2.1.85, and include the EC number annotations, CAZy family and CAZy subfamily annotations we use the command:

cw_query_database cazy/cazyme.db csv \
   --ec --sequences \
   --classes GH,CE,CBM \
   --kingdoms bacteria \
   --ec_filter "3.2.1.23,3.2.1.37,3.2.1.85" \
   --include family subfamily ec