API Reference

Query models and clients

Shared results and clients for external biological resources.

query.QueryResult: Retain normalized provenance alongside an unmodified provider response.
query.QueryError: Report a provider or input error that can be shown to a CLI user.
query.PubTatorClient: Access the documented PubTator 3 search and autocomplete endpoints.

Gene, variant, and biomedical literature queries.

query.query_gene(): Query MyGene while retaining its raw response and build metadata.
query.query_variant(): Query MyVariant while retaining its raw response and source metadata.
query.query_literature(): Search PubTator using either free text or normalized biological entities.

Classes for projects, archives, and scientific files.

project.ProjectManager
filemanager.Archiver: Archive folders and files.
filemanager.FileOrganizer: A utility class for organizing files in standard directories like Downloads and Documents.

project.ProjectManager.new_project(): Create a new project and update its metadata in the .labrat file.
project.ProjectManager.list_projects(): List all projects stored in the .labrat file.
project.ProjectManager.update_project(): Update the last modified timestamp for an existing project.
project.ProjectManager.list_project_files(): List all files within the given project directory.
project.ProjectManager.archive_project(): Archive a project directory to a timestamped archive folder.
project.ProjectManager.add_template(): Add a new project template.
project.ProjectManager.delete_project(): Archive and delete a project directory.

filemanager.FileOrganizer.move_file(): Move a file to the destination directory, handling duplicates and logging actions.
filemanager.FileOrganizer.organize_by_year(): Organize files into subfolders by year based on the last modified timestamp.
filemanager.FileOrganizer.organize_documents(): Organize documents into subfolders by type and year.
filemanager.FileOrganizer.organize_archives(): Organize archives into subfolders by compression type.
filemanager.FileOrganizer.organize_files(): Organize files into standard categories (e.g., Pictures, Videos).
filemanager.FileOrganizer.move_specific_files(): Move files containing a specific keyword in their names to a designated folder.
filemanager.FileOrganizer.organize_science_files(): Organize scientific data files into a dedicated research files folder.
filemanager.FileOrganizer.organize_all(): Execute all organizational tasks in sequence.

DNA and protein sequence utilities.

genetics.atgc_content(): Calculate the nucleotide composition of a DNA sequence.
genetics.complementary_dna(): Create the complementary DNA sequence.
genetics.dna2aminoacid(): Convert a DNA sequence from a FASTA file to an amino acid sequence.

Common concentration and optical calculations.

math.calculate_molarity(): Calculate the molarity of a solution given moles and liters or mL.
math.dilute_stock(): Dilute a stock concentration.
math.mass_recorder(): Record the mass of different items.
math.refractive_index_prism(): Calculate the refractive index of prism.
math.transmittance_to_absorbance(): Convert transmittance to absorbance.