Skip to main content

A package for creating and managing sample identifiers in comparative -omics datasets.

Project description

Build Status Coverage Status

cual-id paper

Preprint outlining implications and uses of cual-id. cual-id globally unique, correctable, and human-friendly sample identifiers for comparative -omics studies.

Peer review is currently in progress


pip install cual-id


Getting help

cual-id --help

Creating a list of IDs

cual-id create ids 42 # writes 42 ids to stdout
cual-id create ids 42 > my-ids.txt # writes 42 ids to my-ids.txt

Creating a PDF of ID labels

If you need to label sample containers with stickers, you can create a printable PDF for those stickers. Currently the only sticker sheet format supported is a 4 by 9 sheet. We designed this printout for Electronic Imaging Materials #80402 label sheets. When printing PDFs make sure to check Actual Size in the print dialog box.

cual-id create labels my-ids.txt --output-pdf my-labels.pdf
cual-id create labels my-ids.txt --output-pdf my-labels.pdf --suppress-ids # don't print the ids, only the barcodes
cual-id create labels my-ids.txt --output-pdf my-labels.pdf --barcode none # don't print barcodes, just the ids

Correcting a list of ids

cual-id fix examples/modified-ids.txt --correct-ids examples/ids.txt # report fixed, unfixable and duplicates, the default
cual-id fix examples/modified-ids.txt --correct-ids examples/ids.txt --show FN # report only fixed and unfixable IDs

Result code definitions

  • D: duplicate

  • F: fixed

  • N: not fixable

  • V: valid (didn’t need correction)

Output Format

input-id <tab> output-id <tab> result-codes

For example:

1a529f8b     1a529f88        F
d60d0e2b     d60d0c2b        F
439628o9     43962809        F
439628o9     43962809        DF
df47deb4     df47deba        F

Python API

from cualid import create_ids
create_ids(10) # Creates a list of tuples containing a UUID and a cualid

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

cual-id-0.9.1.tar.gz (8.9 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page