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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

Install

pip install cual-id

Usage

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


Release history Release notifications

This version
History Node

0.9.1

History Node

0.9.0

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Filename, size & hash SHA256 hash help File type Python version Upload date
cual-id-0.9.1.tar.gz (8.9 kB) Copy SHA256 hash SHA256 Source None Oct 16, 2015

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