# API Reference


## Query models and clients


Shared results and clients for external biological resources.


[query.QueryResult](query.QueryResult.md#labrat.query.QueryResult)  
Retain normalized provenance alongside an unmodified provider response.

[query.QueryError](query.QueryError.md#labrat.query.QueryError)  
Report a provider or input error that can be shown to a CLI user.

[query.PubTatorClient](query.PubTatorClient.md#labrat.query.PubTatorClient)  
Access the documented PubTator 3 search and autocomplete endpoints.


## Biological queries


Gene, variant, and biomedical literature queries.


[query.query_gene()](query.query_gene.md#labrat.query.query_gene)  
Query MyGene while retaining its raw response and build metadata.

[query.query_variant()](query.query_variant.md#labrat.query.query_variant)  
Query MyVariant while retaining its raw response and source metadata.

[query.query_literature()](query.query_literature.md#labrat.query.query_literature)  
Search PubTator using either free text or normalized biological entities.


## Project and file management


Classes for projects, archives, and scientific files.


[project.ProjectManager](project.ProjectManager.md#labrat.project.ProjectManager)  

[filemanager.Archiver](filemanager.Archiver.md#labrat.filemanager.Archiver)  
Archive folders and files.

[filemanager.FileOrganizer](filemanager.FileOrganizer.md#labrat.filemanager.FileOrganizer)  
A utility class for organizing files in standard directories like Downloads and Documents.


## ProjectManager methods


[project.ProjectManager.new_project()](project.ProjectManager.new_project.md#labrat.project.ProjectManager.new_project)  
Create a new project and update its metadata in the .labrat file.

[project.ProjectManager.list_projects()](project.ProjectManager.list_projects.md#labrat.project.ProjectManager.list_projects)  
List all projects stored in the .labrat file.

[project.ProjectManager.update_project()](project.ProjectManager.update_project.md#labrat.project.ProjectManager.update_project)  
Update the last modified timestamp for an existing project.

[project.ProjectManager.list_project_files()](project.ProjectManager.list_project_files.md#labrat.project.ProjectManager.list_project_files)  
List all files within the given project directory.

[project.ProjectManager.archive_project()](project.ProjectManager.archive_project.md#labrat.project.ProjectManager.archive_project)  
Archive a project directory to a timestamped archive folder.

[project.ProjectManager.add_template()](project.ProjectManager.add_template.md#labrat.project.ProjectManager.add_template)  
Add a new project template.

[project.ProjectManager.delete_project()](project.ProjectManager.delete_project.md#labrat.project.ProjectManager.delete_project)  
Archive and delete a project directory.


## FileOrganizer methods


[filemanager.FileOrganizer.move_file()](filemanager.FileOrganizer.move_file.md#labrat.filemanager.FileOrganizer.move_file)  
Move a file to the destination directory, handling duplicates and logging actions.

[filemanager.FileOrganizer.organize_by_year()](filemanager.FileOrganizer.organize_by_year.md#labrat.filemanager.FileOrganizer.organize_by_year)  
Organize files into subfolders by year based on the last modified timestamp.

[filemanager.FileOrganizer.organize_documents()](filemanager.FileOrganizer.organize_documents.md#labrat.filemanager.FileOrganizer.organize_documents)  
Organize documents into subfolders by type and year.

[filemanager.FileOrganizer.organize_archives()](filemanager.FileOrganizer.organize_archives.md#labrat.filemanager.FileOrganizer.organize_archives)  
Organize archives into subfolders by compression type.

[filemanager.FileOrganizer.organize_files()](filemanager.FileOrganizer.organize_files.md#labrat.filemanager.FileOrganizer.organize_files)  
Organize files into standard categories (e.g., Pictures, Videos).

[filemanager.FileOrganizer.move_specific_files()](filemanager.FileOrganizer.move_specific_files.md#labrat.filemanager.FileOrganizer.move_specific_files)  
Move files containing a specific keyword in their names to a designated folder.

[filemanager.FileOrganizer.organize_science_files()](filemanager.FileOrganizer.organize_science_files.md#labrat.filemanager.FileOrganizer.organize_science_files)  
Organize scientific data files into a dedicated research files folder.

[filemanager.FileOrganizer.organize_all()](filemanager.FileOrganizer.organize_all.md#labrat.filemanager.FileOrganizer.organize_all)  
Execute all organizational tasks in sequence.


## Genetics


DNA and protein sequence utilities.


[genetics.atgc_content()](genetics.atgc_content.md#labrat.genetics.atgc_content)  
Calculate the nucleotide composition of a DNA sequence.

[genetics.complementary_dna()](genetics.complementary_dna.md#labrat.genetics.complementary_dna)  
Create the complementary DNA sequence.

[genetics.dna2aminoacid()](genetics.dna2aminoacid.md#labrat.genetics.dna2aminoacid)  
Convert a DNA sequence from a FASTA file to an amino acid sequence.


## Laboratory math


Common concentration and optical calculations.


[math.calculate_molarity()](math.calculate_molarity.md#labrat.math.calculate_molarity)  
Calculate the molarity of a solution given moles and liters or mL.

[math.dilute_stock()](math.dilute_stock.md#labrat.math.dilute_stock)  
Dilute a stock concentration.

[math.mass_recorder()](math.mass_recorder.md#labrat.math.mass_recorder)  
Record the mass of different items.

[math.refractive_index_prism()](math.refractive_index_prism.md#labrat.math.refractive_index_prism)  
Calculate the refractive index of prism.

[math.transmittance_to_absorbance()](math.transmittance_to_absorbance.md#labrat.math.transmittance_to_absorbance)  
Convert transmittance to absorbance.