by @LonsBio

FASTQ with Emoji = FASTQE 🤔

Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason.

Given a fastq file in Illumina 1.8+/Sanger format, calculate the mean (rounded) score for each position and print a corresponding emoji!

https://fastqe.com/

History

FASTQE started out as part of PyCon Au presentations:

PyCon Au 2016 - Python for science, side projects and stuff!
PyCon Au 2017 - Lightning Talk

Versions

version 0.0.1 at PyCon Au 2016:
- Mean position per read
version 0.0.2 at PyconAu 2017:
- update emoji map
- Max and minimum scores per position added
- Wrapper code based on early version of Bionitio added
- prepare for PyPi
version 0.1.0 July 2018
- clean up code
- add binning

Limitations

Reads up to 500bp only
Same emoji for all scores above 41

Quickstart

pip install fastqe

fastqe test.fastq

fastqe --min test.fastq

fastqe --max test.fastq

Usage

fastqe can display usage information on the command line via the -h or --help argument:

% `fastqe`-py -h
usage: fastqe [-h] [--minlen N] [--version] [--mean] [--bin] [--min] [--max]
              [--log LOG_FILE] [--scale]
              [FASTQ_FILE [FASTQ_FILE ...]]

Read one or more FASTQ files, compute quality stats for each file, print as
emoji... for some reason.

positional arguments:
  FASTQ_FILE      Input FASTQ files

optional arguments:
    -h, --help      show this help message and exit
    --minlen N      Minimum length sequence to include in stats (default 0)
    --version       show program's version number and exit
    --mean          show mean quality per position (DEFAULT)
    --bin           use binned scores
    --min           show minimum quality per position
    --max           show maximum quality per position
    --log LOG_FILE  record program progress in LOG_FILE
    --scale         show relevant scale in output

Licence

This program is released as open source software under the terms of MIT License

Dependencies

pyemojify
BioPython
NumPy

Roadmap

Rearrange emoji to use more realistic ranges (i.e > 60 use uncommon emoji) and remove inconsistencies
Add conversion to emoji sequence format, with/without binning, for compressed fastq data
Rewrite conversion to standalone function for use in iPython etc.
Teaching resources
Test data and unit tests
Add FASTA mode for nucleotide and proteins emoji
MultiQC plugin

Scale

Use the --scale option to include in output.

0 ! 🚫
1 " ❌
2 # 👺
3 $ 💔
4 % 🙅
5 & 👾
6 ' 👿
7 ( 💀
8 ) 👻
9 * 🙈
10 + 🙉
11 , 🙊
12 - 🐵
13 . 😿
14 / 😾
15 0 🙀
16 1 💣
17 2 🔥
18 3 😡
19 4 💩
20 5 ⚠️
21 6 😀
22 7 😅
23 8 😏
24 9 😊
25 : 😙
26 ; 😗
27 < 😚
28 = 😃
29 > 😘
30 ? 😆
31 @ 😄
32 A 😋
33 B 😄
34 C 😝
35 D 😛
36 E 😜
37 F 😉
38 G 😁
39 H 😄
40 I 😎
41 J 😍

Binned scale:

0 ! 🚫
1 " 🚫
2 # 💀
3 $ 💀
4 % 💀
5 & 💀
6 ' 💀
7 ( 💀
8 ) 💀
9 * 💀
10 + 💩
11 , 💩
12 - 💩
13 . 💩
14 / 💩
15 0 💩
16 1 💩
17 2 💩
18 3 💩
19 4 💩
20 5 ⚠️
21 6 ⚠️
22 7 ⚠️
23 8 ⚠️
24 9 ⚠️
25 : 😄
26 ; 😄
27 < 😄
28 = 😄
29 > 😄
30 ? 😆
31 @ 😆
32 A 😆
33 B 😆
34 C 😆
35 D 😎
36 E 😎
37 F 😎
38 G 😎
39 H 😎
40 I 😍
41 J 😍

ahasson/fastqe