Tutorials on configuring cazy_webscraper to retrieve data from UniProt

cazy_webscraper can be configured to retrieve user specified data sets from UniProt for specific date sets of CAZymes in a local CAZyme database. Many of the same configuration options apply to the retrieval of protein data from CAZy, UniProt, GenBank and PDB.

Note

cazy_webscraper retrieves protein data from UniProt for CAZymes in a local CAZyme database. It will not add new proteins to the database.

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 data from UniProt. 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_get_uniprot_data - 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/expand/uniprot/get_uniprot_data.py.

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

All data retrieved from UniProt by cw_get_uniprot_data is added to the local CAZyme database.

Configuration via the command line

cw_get_uniprot_data only requires one argument: the path to the local CAZyme database created using cazy_webscraper.

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

cazy_webscraper <path to the local CAZyme db>

For example, if our database was stored in cazy/cazyme.db, we would used:

cazy_webscraper cazy/cazyme.db

Note

Make sure cw_get_uniprot_data is pointed directly at the database file.

When no optional arguments are provided, the default behaviour is invoked. The default behaviour is to:

  • Retrieve protein data for all CAZymes in the local CAZyme db

  • Retrieve UniProt protein accessions and protein names

  • Not retrieve EC number, PDB accessions and protein sequences

Options configurable at the command line

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

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

  • Enable retrieving EC number annotations

  • Enable retrieving PDB accessions

  • Enable retrieving protein amino acid sequences

  • Enable updating protein sequences in the local CAZyme database if newer versions are retrieved from UniProt

  • Enable verbose logging during the operation of the webscraper

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

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 retrieve data from UniProt.

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 then use the command:

cw_get_uniprot_data cazy/cazyme.db --classes GH,CE

OR

cw_get_uniprot_data cazy/cazyme.db --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 use the following command:

cw_get_uniprot_data cazy/cazyme.db --families PL1,PL2,PL3

Warning

cw_get_uniprot_data 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:

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

AND

cw_get_uniprot_data cazy/cazyme.db --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 UniProt 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_get_uniprot_data cazy/cazyme.db --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_get_uniprot_data command. The command we would use would be:

cw_get_uniprot_data cazy/cazyme.db --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_get_uniprot_data will retrieval CAZymes from all strains of the species.

Applying EC number filter

The retrieval of protein data from UniProt 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_get_uniprot_data cazy/cazyme.db --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 UniProt will be retrieved. These flags can be used with any combination of --ec, --pdb, --sequence, --update_seq to customise what data is retrieved from UniProt and added to the local CAZyme database.

Below we run through 3 example commands of combining these flags, and the resulting behaviour.

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

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

Example 2: To retrieve EC numbers, PDB accessions and taxonomies for all CAZymes in GH and which are derived from Aspegillus and Trichoderma species we use the command:

cw_get_uniprot_data cazy/cazyme.db --pdb --ec --classes GH --genera Aspegillus,Trichoderma --taxonomy

Example 3: To retrieve EC numbers and sequences 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_get_uniprot_data cazy/cazyme.db --ec --sequences --classes GH,CE,CBM --kingdoms bacteria --ec_filter "3.2.1.23,3.2.1.37,3.2.1.85"

Providing a list of accessions

Instead of retrieving protein data for all CAZymes matching a defined set of criteria, cw_get_uniprot_data can retrieve protein data a set of CAZymes defined by their GenBank accession.

The flag --genbank_accessions can be used to provide cw_get_uniprot_data a list of GenBank accessions to identify the specific set of CAZymes to retrieve protein data for.

The list of respective accessions are provided via a plain text file, with a unique protein accession of each line. The path to this file is then passed to cw_get_uniprot_data via the --genbank_accessions flag.

Warning

--genbank_accessions takes president over the filter flags.

When --genbank_accessions is used, cw_get_uniprot_data will not retrieve any CAZymes from the local database matching a set of criteria.

Therefore, if --genbank_accessions and --classes are used, cw_get_uniprot_data will ignore the --classes flag and only retrieve protein data for the proteins listed in the file provided via the --genbank_accessions.