The genbank module¶

The module genbank contains submodules that handle GenBank files. This includes the retrieval of GenBank files from the NCBI Assembly database, and retrieval of protein annotations (writing out th protein sequences to FASTA files and protein data to a summary dataframe) from GenBank files.

- get_ncbi_genomes

- get_genbank_annotations

get_ncbi_genomes¶

get_ncbi_genomes is a submodule of the genbank, it takes a plain text file containing species scientific names or NCBI taxonomy as input. The script finds the corresponding taxonomy ID or scientific name, as appropriate, as well as retrieve all directly linked accession numbers. The submodule generates a dataframe containing ‘Genus’, ‘Species’, ‘NCBI Taxonomy ID’, and ‘NCBI Accession Number’.

Invoking the script from the command line¶

To invoke get_ncbi_genomes invoke the script get_ncbi_genomes.py, for example, using the following command: python3 get_ncbi_genomes <user_email> <-i path_to_input_.txt> <-o directory_to_store_assemblies> <-d species_dataframe_output_path

Compulsary arguments

-u, --user - Although indicated as optional, Entrez requires an email address must be provided. If not provided the programme will log this as an error and terminate.

Optional arguments

-d, --`dataframe - Specify output path for dataframe, which will be saved as a .csv file (inclusion of file extensions is optional). If not provided dataframe will be written out to STDOUT.

-f, --force - Enable writting in specificed output directory if output directory already exists.

-g, --genbank - Enable or disable downloading of GenBank files.

-h, --help - Display help messages and exit, including listing arguments

-i, --input - Specify input filename (with extension) input file.If only the filename is supplied get_ncbi_genomes.py will only look in the curent working directory, otherwise provide path to input file. If no option is given the default input is taken from STDIN.

-l, --log - Specify name of log file (With extension). If only filename is given, log file will be written out to the current working directory, otherwise provide path including filename. If not option is given no log file will be written out, however, logs will still be printed to the terminal.

-n, --nodelete - Enable not deleting files in existing output directory. If not enabled, output directory exists and writing in output directory is ‘forced’ then files in output directory will not be deleted, and new files will be written to the output directory.

-o, --output - Specify filename (with extension) of output file. If not option is given output will be written to STDOUT.

-r, --retries - Specifiy maximum number of retries before cancelling call to NCBI if a network error is encountered. The default is a maximum of 10 retries. When maximum is reached, a value of ‘NA’ is returned.

-t, --timeout - Specify timeout limit of URL connection when downloading GenBank files. Default is 10 seconds.

-v, --verbose - Enable verbose logging - changes logger level from WARNING to INFO.

get_genbank_annotations¶

get_genbank_annotations is a submodule of the genbank, which reads NCBI GenBank files and retrieves annotations of encoded Proteins. Specifically, get_genbank_annotations parses each genomic assembly contained within the input directory passed the module, during which it identifies a protein by its annotation as a ‘CDS’ feature. The summary data (listed out below) for every protein is written out to a dataframe, with a unique protein in each row. The sequence of each protein is also written out to a FASTA file. Proteins from the same genomic assembly are written out to the same FASTA file, therefore, a singel FASTA file containing the sequences of all the proteins identified within the assembly is created per genomic assembly in the input directory.

Dataframe columns: * ‘Genus’ * ‘Species’ * ‘NCBI Taxonomy ID’ * ‘NCBI Accession Number’ * ‘NCBI Protein ID’ * ‘Locus Tag’ * ‘Gene Locus’ * ‘NCBI Recorded Function’ * ‘Protein Sequence’ * ‘UniProtKB Entry ID’ * ‘UniProt Entry Name’ * ‘UniProtKB Protein Names’ * ‘EC number’ * ‘Length (Aa)’ * ‘Mass (Da)’ * ‘Domains’ * ‘Domain count’ * ‘UniProtKB Linked Protein Families’ * ‘Gene ontology IDs’ * ‘Gene ontology (molecular function)’ * ‘Gene ontology (biological process)’

get_genbank_annotations has been created as a subsequent or complementary module to get_ncbi_genomes and is designed to parse the outputs from get_ncbi_genomes.

Invoking the script from the command line¶

To invoke get_genbank_annotations invoke the script get_genbank_annotations.py, for example, use the following command: python3 get_genbank_annotations <path_to_input_df> <path_to_assemly_dir>

Compulsary arguments

--input_df - Path to the dataframe containing the accession numbers of the genomic assemblies. This dataframe is created by get_ncbi_genomes.

--genbank - Path to directory containing the genomic assemblies listed within the dataframe. Unless they have been moved, this is the output directory from get_ncbi_genomes.