A package for creating and managing sample identifiers in comparative -omics datasets.
Project description
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-idUsage
Getting help
cual-id --helpCreating 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.txtCreating 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 idsCorrecting 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 IDsResult 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
