ESTIMATEERROR.PY(1)

✨ NAME ✨

Okay bestie, meet EstimateError.py 💖 It calculates annotation set error rates, and it is lowkey the most useful little tool for checking how often your annotation sets are messing up 🎀

✨ DESCRIPTION ✨

Here's the usage line, verbatim 💅

usage: EstimateError.py [--version] [-h]  ...

It calculates annotation set error rates. Slay 🔥

🎀 help

• --version — shows the program's version number and then exits 🦋
• -h, --help — shows the help message and then exits 🫶

🧚 subcommands

Estimation method 🌈 (that's the main vibe for both of these)

• set — estimates error statistics within annotation sets 💅
• barcode — calculates pairwise distance metrics of barcode sequences ✨

🦋 output files

Here's what each output file gives you, bestie 💜

• error-position — estimated error by read position 🌸
• error-quality — estimated error by the quality score that was assigned within the input file 🎀
• error-nucleotide — estimated error by nucleotide 🍓
• error-set — estimated error by annotation set size 🔥
• distance-set — pairwise hamming distances by annotation set 🧚
• threshold-set — thresholds from pairwise hamming distances for annotation sets 👑
• distance-barcode — estimated error by pairwise hamming distances. 🦋
• threshold-barcode — thresholds from pairwise hamming distances for clustering barcodes 💖

👑 output fields

These are the columns you'll see, and they are giving main character energy 💅

• POSITION — read position, using base zero indexing 🌈
• Q — Phred quality score ✨
• OBSERVED — observed nucleotide value 🫶
• REFERENCE — consensus nucleotide for the barcode read group 💜
• SET_COUNT — barcode read group size 🎀
• REPORTED_Q — mean Phred quality score reported within the input file for the given position, quality score, nucleotide or read group 🌸
• MISMATCHES — count of observed mismatches from consensus for the given position, quality score, nucleotide or read group 💀
• OBSERVATIONS — total count of observed values for each position, quality score, nucleotide or read group size 🍓
• ERROR — estimated error rate 🔥
• EMPIRICAL_Q — estimated error rate converted to a Phred quality score 👑
• ALL — histogram (count) of the all pairwise distance distribution 🦋
• DTN — histogram (count) of the distance to nearest distribution 🧚
• DISTANCE — length normalized hamming distance 💖

✨ AUTHOR ✨

Andreas Tille wrote this manpage for the Debian distribution 🌸 and it can be used for any other usage of the program 🫶

Bestie, that's the whole page 💜 We ate EstimateError.py 0.6.0 from May 2020 and left no crumbs 💅✨