loompy

library3.0.8pypypi✓ verified 85d ago

A Python library for working with Loom file format (version 3.0.8), which is used for storing single-cell RNA-seq data. It supports reading, writing, and creating Loom files with sparse matrices, variable-length string attributes, and provides a command-line tool for creating Loom files from FASTQ. Release cadence is irregular.

data serialization

pip install loompy

github ↗package ↗

INSTALL

IMPORT

SIG · LOOMPY

loompy

datapythonv3.0.8

Install

12.2s avg

Import

5050ms

Disk

434MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v3.0.8 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 12.2s · import 5.050s · 429MB

434MB installed

● package 434MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

loompy

✓ import loompy

✗ from loompy import LoomFile

LoomFile is not a top-level class; use loompy.connect() or loompy.create()

connect

✓ import loompy; ds = loompy.connect('file.loom')

✗ from loompy import connect

connect is a function, not a module; import the package and use it as attribute

Create a Loom file with a small matrix and read it back.

import loompy import numpy as np # Create a minimal loom file row_attrs = {'Gene': ['A', 'B']} col_attrs = {'CellID': ['cell1', 'cell2']} matrix = np.array([[1, 2], [3, 4]], dtype='float32') loompy.create('test.loom', matrix, row_attrs, col_attrs) # Read it backts = loompy.connect('test.loom') print(fts.shape) fts.close()

loom --version

Debug

Known issues

breakingloompy 3.0.0 introduced a major API overhaul: old classes like LoomFile are replaced with connect(), create(), etc. Code written for loompy 2.x will not run without modification.

fix

Migrate from LoomFile('file.loom', 'r') to loompy.connect('file.loom'), and from creating with LoomFile('file.loom', 'w') to loompy.create().

affects: >=3.0.0

gotchaWhen opening a Loom file in write mode using connect() with mode='w', the file is overwritten. Ensure you have a backup.

fix

Use mode='r+' to read/write without truncation, or check file existence beforehand.

affects: all

deprecatedSome older API methods like loompy.LoomFile and loompy.File are deprecated in 3.0.x and may be removed in future versions.

fix

Replace with loompy.connect() for reading/writing and loompy.create() for creating new files.

affects: >=3.0.0

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'loompy'

loompy is not installed.

fix

Install with pip install loompy

AttributeError: module 'loompy' has no attribute 'LoomFile'

Using the deprecated LoomFile class which was removed in version 3.0.0.

fix

Use loompy.connect() to open files and loompy.create() to create them.

OSError: Unable to open file (unable to open file: name = 'test.loom', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Trying to read a file that does not exist.

fix

Check that the file path is correct and the file exists.

ValueError: Shape mismatch. Matrix has shape (100, 200) but row_attrs has length 50

The dimensions of the matrix do not match the number of row attributes.

fix

Ensure that the number of rows in the matrix equals the length of row attribute values, and columns equal length of column attributes.

Upgrade

Version history

3.0.8latest on PyPI · released Jan 10, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

5 hits · last 30 days

node

Resources

githubhttps://github.com/linnarsson-lab/loompy ↗

packagehttps://pypi.org/project/loompy/ ↗