prepare.py creates a tsv file for ingestion by scientific workflows.
It is a super stripped down version of bactopia-prepare.py from https://github.com/bactopia/bactopia-py. I butchered the script for my own needs. Full credit goes to rpetit3 for writing this script. Please cite his work if you use this script. Make sure to checkout the Bactopia!
- rich
- rich-click
pip install rich rich-click
Then either git clone this report or dub-get it.
Example *.fastq.gz FASTQ files:
prepare.py --path fastqs/
sample runtype r1 r2
sample01 paired-end fastqs/sample01_R1.fastq.gz fastqs/sample01_R2.fastq.gz
sample02 single-end fastqs/sample02.fastq.gz
sample03 paired-end fastqs/sample03_R1.fastq.gz fastqs/sample03_R2.fastq.gz
Example *_001.fastq.gz FASTQ files:
prepare.py --path fastqs/ --fastq-ext '_001.fastq.gz'
sample runtype r1 r2
sample01 paired-end fastqs/sample01_R1_001.fastq.gz fastqs/sample01_R2_001.fastq.gz
sample02 paired-end fastqs/sample02_R1_001.fastq.gz fastqs/sample02_R2_001.fastq.gz
sample03 paired-end fastqs/sample03_R1_001.fastq.gz fastqs/sample03_R2_001.fastq.gz
Example *.fq.gz FASTQ files:
prepare.py --path fastqs --fastq-ext '.fq.gz'
sample runtype r1 r2
sample01 single-end fastqs/sample01.fq.gz
sample02 single-end fastqs/sample02.fq.gz
sample03 single-end fastqs/sample03.fq.gz
Example Nanopore FASTQ files:
prepare.py --path fastqs/ --ont
sample runtype r1 r2
sample01 ont fastqs/sample01.fastq.gz
sample02 ont fastqs/sample02.fastq.gz
sample03 ont fastqs/sample03.fastq.gz
Example changing the separator, do this if you have underscores in your sample names and you want SE reads:
prepare.py --path ext/ --fastq-separator '.'
sample runtype r1 r2
sample_01 single-end fastqs/sample_01.fastq.gz
sample_02 single-end fastqs/sample_02.fastq.gz
sample_03 single-end fastqs/sample_03.fastq.gz
Because I didn't want to reinvent the wheel, and rpetit3 is a fantastic coder. So I went looking for something I could rework (butcher).
https://github.com/bactopia/bactopia-py
Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems. 5 (2020), https://doi.org/10.1128/mSystems.00190-20.