API Reference

Math Functions

labrat.math.functions

Reusable math functions for scientists.

calculate_molarity(moles, volume, units)

Calculate the molarity of a solution given moles and liters or mL.

Parameters:

Name	Type	Description	Default
moles	[type]	[description]	required
volume	[type]	[description]	required
units	[type]	[description]	required

Raises:

Type	Description
ValueError	[description]

Returns:

Type	Description

dilute_stock(cI, vI, **values)

Dilute a stock concentration.

Parameters:

Name	Type	Description	Default
cI	[type]	[description]	required
vI	[type]	[description]	required

Raises:

Type	Description
UserWarning	[description]
KeyError	[description]

Returns:

Type	Description

mass_recorder(grams, item, sigfigs)

Record the mass of different items.

Parameters:

Name	Type	Description	Default
grams	[type]	[description]	required
item	[type]	[description]	required
sigfigs	[type]	[description]	required

Raises:

Type	Description
ValueError	[description]

refractive_index_prism(prism, deviation, angle_measurement)

Calculate the refractive index of prism.

This function uses the angle of prism and minimum angle of deviation.

Parameters:

Name	Type	Description	Default
prism	[type]	[description]	required
deviation	[type]	[description]	required
angle_measurement	[type]	[description]	required

Raises:

Type	Description
ValueError	[description]

Returns:

Type	Description

transmittance_to_absorbance(transmittance)

Convert transmittance to absorbance.

Parameters:

Name	Type	Description	Default
transmittance	[type]	[description]	required

Raises:

Type	Description
ValueError	[description]

Returns:

Type	Description

Genetics

labrat.genetics.dna_analysis

DNA Analysis functions.

atgc_content(dna_sequence)

Calculate the nucleotide composition of a DNA sequence.

Counts the occurrences of each nucleotide (A, T, G, C) in the sequence. Non-standard nucleotides are ignored in the count.

Parameters:

Name	Type	Description	Default
dna_sequence	str	The DNA sequence to analyze. Case-insensitive.	required

Returns:

Name	Type	Description
dict	Dict[str, int]	A dictionary with keys ‘A’, ‘T’, ‘G’, ‘C’ and their counts as values.

Example

atgc_content(“ATGCGAT”)

complementary_dna(dna_sequence)

Create the complementary DNA sequence.

Generates the complementary strand by replacing each nucleotide with its complement: A↔T and G↔C. Non-standard nucleotides are replaced with ‘X’.

Parameters:

Name	Type	Description	Default
dna_sequence	str	The DNA sequence to complement. Case-insensitive.	required

Returns:

Name	Type	Description
str	str	The complementary DNA sequence as a string.

Example

complementary_dna(“ATGC”) ‘TACG’ complementary_dna(“ATGN”) ‘TACGX’

labrat.genetics.protein_analysis

Protein Analysis functions.

dna2aminoacid(fasta_file, codons=None)

Convert a DNA sequence from a FASTA file to an amino acid sequence.

This function reads a FASTA-formatted file, extracts the DNA sequence (skipping the header line that starts with ‘>’), and translates it into an amino acid sequence using the genetic code. The sequence is processed in groups of three nucleotides (codons), and each codon is looked up in the codon dictionary to determine the corresponding amino acid.

Parameters:

Name	Type	Description	Default
fasta_file	str	Path to the FASTA file containing the DNA sequence.	required
codons	dict	Dictionary mapping 3-letter DNA codons to single-letter amino acid codes. Defaults to the standard genetic code.	None

Returns:

Name	Type	Description
str	str	The translated amino acid sequence as a single-letter code string.

Raises:

Type	Description
FileNotFoundError	If the FASTA file cannot be found.
KeyError	If an invalid codon (not in the dictionary) is encountered.
ValueError	If the DNA sequence length is not a multiple of 3.

Example

sequence = dna2aminoacid(“sequence.fasta”) print(sequence) MKTAYIAKQR…

Project Management

labrat.project.projectmanager

ProjectManager

labrat_file property

Get the path to the .labrat config file.

Returns:

Name	Type	Description
Path		Path to config.json inside the .labrat directory.

__init__(username=None)

Initialize the project manager with a default username.

Parameters:

Name	Type	Description	Default
username	str	The user’s name. Defaults to the value in .labrat or ‘default_user’.	None

add_template(name, url)

Add a new project template.

Parameters:

Name	Type	Description	Default
name	str	The name of the template.	required
url	str	The repository URL of the template.	required

Raises:

Type	Description
ValueError	If the template name already exists.

archive_project(project_path, archive_base_dir)

Archive a project directory to a timestamped archive folder.

Parameters:

Name	Type	Description	Default
project_path	str or Path	The path to the project directory.	required
archive_base_dir	str or Path	The base directory for storing archives.	required

Returns:

Name	Type	Description
str		Path to the created archive directory.

delete_project(project_path, archive_base_dir)

Archive and delete a project directory.

Parameters:

Name	Type	Description	Default
project_path	str or Path	The path to the project directory.	required
archive_base_dir	str or Path	The base directory for storing archives.	required

Raises:

Type	Description
ValueError	If the project path does not exist or is not a directory.

list_project_files(project_path)

List all files within the given project directory.

Parameters:

Name	Type	Description	Default
project_path	str	The path to the project.	required

Returns:

Name	Type	Description
list		A list of file paths within the project directory.

list_projects()

List all projects stored in the .labrat file.

Returns:

Name	Type	Description
list		A list of project metadata dictionaries.

new_project(project_type, project_name, project_path, description)

Create a new project and update its metadata in the .labrat file.

Parameters:

Name	Type	Description	Default
project_type	str	The type of project.	required
project_name	str	The name of your project.	required
project_path	str	The destination path of the project.	required
description	str	A description of the project.	required

Raises:

Type	Description
ValueError	If the project type is not valid.

update_project(project_path)

Update the last modified timestamp for an existing project.

Parameters:

Name	Type	Description	Default
project_path	str	The path to the project to update.	required

File Management

labrat.filemanager.archive

Archiver

Archive folders and files.

__init__(source_dir, archive_dir)

Initialize logger and archive parameters.

Parameters:

Name	Type	Description	Default
source_dir	str or Path	The directory to copy or archive.	required
archive_dir	str or Path	The destination directory for the archive.	required

archive()

Perform the archive by copying the source directory to the archive directory and then creating a zip file of the archived folder.

Raises:

Type	Description
SameFileError	If the source and destination are the same.
OSError	For other filesystem-related errors.

get_archive_dir(base_dir, project_name) staticmethod

Generate a timestamped archive directory path.

Parameters:

Name	Type	Description	Default
base_dir	str or Path	The base directory where archives are stored.	required
project_name	str	The name of the project being archived.	required

Returns:

Name	Type	Description
Path		A path to the timestamped archive directory.

labrat.filemanager.organize

FileOrganizer

A utility class for organizing files in standard directories like Downloads and Documents. Designed for integration into the labrat tool.

__init__()

Initialize the FileOrganizer class with default directories.

move_file(src_file, dest_dir)

Move a file to the destination directory, handling duplicates and logging actions.

Parameters:

Name	Type	Description	Default
src_file	Path	The source file to move.	required
dest_dir	Path	The destination directory where the file will be moved.	required

move_specific_files(keyword='specific')

Move files containing a specific keyword in their names to a designated folder.

Parameters:

Name	Type	Description	Default
keyword	str	Keyword to match in filenames. Default is ‘specific’.	'specific'

organize_all()

Execute all organizational tasks in sequence.

organize_archives()

Organize archives into subfolders by compression type.

organize_by_year(file_path, base_dir)

Organize files into subfolders by year based on the last modified timestamp.

Parameters:

Name	Type	Description	Default
file_path	Path	The file to organize.	required
base_dir	Path	The base directory where files are organized.	required

organize_documents()

Organize documents into subfolders by type and year.

organize_files()

Organize files into standard categories (e.g., Pictures, Videos).

organize_science_files(science_dir=None)

Organize scientific data files into a dedicated research files folder.

Handles common scientific file formats including: - Bioinformatics: fastq, fasta, sam, bam, vcf, bed, gff, gtf - Astronomy: fits, hdf5, nc (NetCDF) - General: csv, tsv, json, h5, parquet - Computational: ipynb, py, r, R

Parameters:

Name	Type	Description	Default
science_dir	Path	Custom directory for science files. Defaults to Documents/Research_Data.	None