https://github.com/rhpvorderman/phred-to-error-rate
Convert FASTQ phred scores to probabilities
https://github.com/rhpvorderman/phred-to-error-rate
Last synced: 3 months ago
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Convert FASTQ phred scores to probabilities
- Host: GitHub
- URL: https://github.com/rhpvorderman/phred-to-error-rate
- Owner: rhpvorderman
- License: mit
- Created: 2023-09-04T14:48:38.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-09-05T12:10:33.000Z (over 1 year ago)
- Last Synced: 2025-01-17T08:43:57.951Z (4 months ago)
- Language: C
- Size: 9.77 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# phred-to-error-rate
Convert FASTQ phred scores to probabilities
## Calculating the score
Actually calculating the score requires calculating an exponent of 10.
This is a lot slower than doing the lookup. Doing this is not recommended.
## Using a lookup table
FASTQ phred scores have a maximum of 94 discrete values. The lower bound is 33
the upper bound is 126. The current fastest
way is to use a lookup table. One can be easily generated in python:
```python3
PHRED_TO_SCORE_LOOKUP = [10 ** (-(i -33) / 10) for i in range (127)]
```
Using [dnaio](https://github.com/marcelm/dnaio) one can easily calculate
the average probability for each read:
```python3
import math
import dnaio
PHRED_TO_SCORE_LOOKUP = [10 ** (-(i -33) / 10) for i in range (127)]
for read in dnaio.open("my.fastq"):
phreds = read.qualities_as_bytes()
total_expected_errors = 0.0
for phred in phreds: # iterating over bytes gives integers
total_expected_errors += PHRED_TO_SCORE_LOOKUP[phred]
average_error_rate = total_expected_errors / len(read)
read_phred_score = -10 * math.log10(average_error_rate)
```
This is how to do it in C.
```C
#include
#include
static inline double
average_error_rate(const uint8_t *phreds, size_t phreds_length) {
const uint8_t *end_ptr = phreds + phreds_length;
const uint8_t *cursor = phreds;
double error_rate = 0.0;
while (cursor < end_ptr) {
uint8_t phred = *cursor - 33;
/* Because phred is unsigned, we only have to check the upper bound */
if (phred > 93) {
return -1.0; // Error rate should always be positive, so this is a good error value.
}
error_rate += SCORE_TO_ERROR_RATE[phred];
cursor += 1;
}
return error_rate / (double)phreds_length;
}
```
Code to generate score_to_error_rate.h is included
[here](score_to_error_rate.py). An already produced example can be obtained
[here](score_to_error_rate.h).