Tutorials on configuring cazy_webscraper
to retrieve data from PDB
cazy_webscraper
can be configured to retrieve protein structures files user specified 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.
BioPython
is used to perform the retrieval of protein structure files from PDB. The retrieved structure
files are written to the disk, not into the local CAZyme database.
> Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., … others. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423.
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 structured from PDB. 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 PDB data call it using cw_get_pdb_structures
- 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/pdb/get_pdb_structures.py
.
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.
From this point on, we will be discussed the cw_get_pdb_structures
, which is the entry point for
retrieving data from PDB. We also presume you are comfortable configuring cazy_webscraper
for the
scraping of data from CAZy.
Configuration via the command line
cw_get_pdb_structures
has two required argument:
* The path to the local CAZyme database created using cazy_webscraper
* The structure file formats to retrieve the data from PDB in
The accepted structure file formats are: * mmCif (default, PDBx/mmCif file), * pdb (format PDB), * xml (PDBML/XML format), * mmtf (highly compressed), * bundle (PDB formatted archive for large structure}
Any combination of file formats can be provided to cw_get_pdb_structures
to download every file type for each PDB accession in the local CAZyme database. To list multiple file formats, separate each file format with a single space (’ ‘). For example, to download the mmCif and xml files for every PDB accession in a local CAZyme database (located at cazy/cazyme_db.db
), use the following command:
cw_get_pdb_structures cazy/cazyme_db.db mmCif xml
Warning
The file formats are case sensitive. For example, make sure to use ‘mmCif’ not ‘mmcif’.
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
Options configurable at the command line
CAZymes of interest can be defined via providing:
A set of GenBank accessions
A set of UniProt accessions
CAZy classes
CAZy families
Taxonomic kingdoms
Genera
Species
Strains
EC numbers
Here you can find a full list of the command-line flags and options.
Retrieving protein structures for specific CAZy classes and families
The --classes
and --families
flags from scraping data from CAZy are applied in the extact same way
for retrieving protein structure files from PDB.
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_pdb_structures cazy/cazyme.db mmCif --classes GH,CE
OR
cw_get_pdb_structures cazy/cazyme.db mmCif --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, in mmCif and PDB format, use the
following command:
cw_get_pdb_structures cazy/cazyme.db mmCif pdb --families PL1,PL2,PL3
Warning
cw_get_pdb_structures
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_pdb_structures cazy/cazyme.db mmCif pdb --families PL1,PL2,PL3 --classes GH,CE
AND
cw_get_pdb_structures cazy/cazyme.db mmCif pdb --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 PDB.
For example, if you want to retrieve protein data for all CAZymes in a local CAZyme database from bacterial and eukaryotic species, in pdb and xml formats, then use the command
cw_get_pdb_structures cazy/cazyme.db pdb xml --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_pdb_structures
command. The command
we would use would be:
cw_get_pdb_structures cazy/cazyme.db pdb xml --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_pdb_structures
will retrieval CAZymes from all strains of the species.
Applying EC number filter
The retrieval of protein data from PDB can also be limited to proteins in a local CAZyme database that are annotated with specific EC numbers.
Having previously retrieved EC number annotations from UniProt and adding 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_pdb_structures cazy/cazyme.db pdb --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
cw_get_pdb_structures
will retrieve the PDB structure files 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 PDB structure files will only be retrieved for
CAZymes annotated for all provided EC numbers.
--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 cw_get_pdb_structures
to retrieve
data for protein A. This is because cw_get_pdb_structures
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
, cw_get_pdb_structures
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 structure files will be retrieved from PDB.
Below we run through 3 example commands of combining these flags, and the resulting behaviour.
Example 1: To retrieve PDB structure file for all CAZymes in GH, GT, CE1, CE5 and CE8, and which are derived from baceterial species, and retrieve the files in mmCif and xml format we use the command:
cw_get_pdb_structures cazy/cazyme.db mmCif xml --classes GH,CE --families CE1,CE5,CE8 --kingdoms bacteria
Example 2: To retrieve PDB structure files for all CAZymes in GH and which are derived from Aspegillus and Trichoderma species in bundle format we use the command:
cw_get_pdb_structures cazy/cazyme.db bundle --classes GH --genera Aspegillus,Trichoderma
Example 3: To retrieve PDB structure files 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 retrieve the files in pdb and xml format we use the command:
cw_get_pdb_structures cazy/cazyme.db xml pdb --classes GH,CE,CBM --kingdoms bacteria --ec_filter "3.2.1.23,3.2.1.37,3.2.1.85"
Note
The order the structure file formats are provided does not matter.
Providing a list of accessions
Instead of retrieving protein structure files for all CAZymes matching a defined set of criteria,
cw_get_pdb_structures
can retrieve protein structure files for a set of CAZymes defined by their
GenBank and/or UniProt accession.
The flag --genbank_accessions
can be used to provide cw_get_pdb_structures
a list of GenBank accessions
to identify the specific set of CAZymes to retrieve protein structure files for.
The flag --uniprot_accessions
can be used to provide cw_get_pdb_structures
a list of UniProt accessions
to identify the specific set of CAZymes to retrieve protein structure files for.
In both instances (for --genbank_accessions
and --uniprot_accessions
) 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_pdb_structures
via the respective --genbank_accessions
and --uniprot_accessions
flag.
--genbank_accessions
and --uniprot_accessions
can be used at the same time to define all
CAZymes of interest.
Warning
--genbank_accessions
and --uniprot_accessions
take president over the filter flags.
When either --genbank_accessions
or --uniprot_accessions
is used, cw_get_pdb_structures
will
not retrieve any CAZymes from the local database matching a set of criteria.
Therefore, if --genbank_accessions
and --classes
are used, cw_get_pdb_structures
will ignore
the --classes
flag and only retrieve PDB structure files for the proteins listed in the file provided via
the --genbank_accessions
.