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!
Latest release versions of fastqe are available via pip or BioConda:
pip install fastqe
conda install -c bioconda fastqe
Development version can be isntall from this repository in the master branch.
fastqe can display usage information on the command line via the -h or --help argument:
usage: fastqe [-h] [--minlen N] [--scale] [--version] [--mean]
[--custom CUSTOM_DICT] [--bin] [--noemoji] [--min] [--max]
[--output OUTPUT_FILE] [--long READ_LENGTH] [--log LOG_FILE]
[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)
--scale show relevant scale in output
--version show program's version number and exit
--mean show mean quality per position (DEFAULT)
--custom CUSTOM_DICT use a mapping of custom emoji to quality in
CUSTOM_DICT (🐍🌴)
--bin use binned scores (🚫💀💩⚠️😄😆😎😍)
--noemoji use mapping without emoji (▁▂▃▄▅▆▇█)
--min show minimum quality per position
--max show maximum quality per position
--output OUTPUT_FILE write output to OUTPUT_FILE instead of stdout
--long READ_LENGTH enable long reads up to READ_LENGTH bp long
--log LOG_FILE record program progress in LOG_FILE
fastqe will summarise FASTQ files to display the max, mean and minumum quality using emoji. To convert a file into this format, rather than summarise, you can use the companion program biomojify that will convert both sequence and quality information to emoji:
$ cat test.fq
@ Sequence
GTGCCAGCCGCCGCGGTAGTCCGACGTGGC
+
GGGGGGGGGGGGGGGGGGGGGG!@#$%&%(
$ biomojify fastq test.fq
▶️ Sequence
🍇🍅🍇🌽🌽🥑🍇🌽🌽🍇🌽🌽🍇🌽🍇🍇🍅🥑🍇🍅🌽🌽🍇🥑🌽🍇🍅🍇🍇🌽
😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁😁🚫😄👺💔🙅👾🙅💀
Intall with pip install biomojify, and see the biomojify page for more information: https://github.com/fastqe/biomojify/
fastqe test.fastq
fastqe --min test.fastq
fastqe --max test.fastq
fastqe --max -min -bin test.fastq
This lesson introduces NGS process in the command line using by using the results of FASTQE before and after quality filerting
using fastp:
https://qubeshub.org/publications/1092/2
Rachael St. Jacques, Max Maza, Sabrina Robertson, Guoqing Lu, Andrew Lonsdale, Ray A Enke (2019).
A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!.
NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis, (Version 2.0).
QUBES Educational Resources. doi:10.25334/Q4D172
A Galaxy wrapper is available from the IUC toolshed. Contact your Galaxy Admin if you would like to have it installed. A Galaxy Tutorial using FASTQE is in development.
FASTQE started out as part of PyCon Au presentations:
- PyCon Au 2016 - Python for science, side projects and stuff!
- PyCon Au 2017 - Lightning Talk
- BCC 2020 - Short Presentaion
- 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
- version 0.2.6 July 2020
- refactor code
- add long read support with --long
- add --noemoji for block-based output on systems that don't support emoji
- add --custom for user-defined mapping to emoji
- add --output to redirect to file instead of stdout
- add gzip support
- add redirect from stdin support
- fix bug of dropping position if some sequences are only 0 quality
- Galaxy Wrapper created July 2020
biomojifycreated July 2020- version 0.2.7 2021
- bugfix
- version 0.3.1 2023
- HTML reporting for Galaxy
- version 0.3.3 2024
- Update emoji that render in default fonts with alternatives
Reads up to 500bp onlyRead length above 500bp allowed but must be set by user with--long MAX_LENGTH- Same emoji for all scores above 41
This program is released as open source software under the terms of BSD License
- pyemojify
- BioPython
- NumPy
- 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 datafits into https://github.com/fastqe/biomojify/ - Rewrite conversion to standalone function for use in iPython etc.
- Teaching resources
- Test data and unit tests
-
Add FASTA mode for nucleotide and proteins emojisee https://github.com/fastqe/biomojify/ - MultiQC plugin
-
Galaxy Wrapper: available form the IUC toolshed
Rather convert to emoji than summarise? We've just started biomojify for that: https://github.com/fastqe/biomojify/
- Andrew Lonsdale
- Björn Grüning
- Catherine Bromhead
- Clare Sloggett
- Clarissa Womack
- Helena Rasche
- Maria Doyle
- Michael Franklin
- Nicola Soranzo
- Phil Ewels
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 😍
Use a dictionary of Pyemojify mappings in a text file instead of built in emoji choices:
{
'#': ':no_entry_sign:',
'\"': ':x:',
'!': ':japanese_goblin:',
'$': ':broken_heart:'
}
Emoji characters can also be used directlty instead (experimental):
{
'#': ':no_entry_sign:',
'\"': ':x:',
'!': '👿',
'$': ':broken_heart:'
}