lxzbiotools 0.5.2

Xingze Li's Bioinformatics Analysis Scripts

Introduction

lxzbiotools contains some bioinformation data processing scripts.

Obviously, it is not perfect, so it will be updated later until it is strong enough

Install

pip3 install lxzbiotools

Use

$ python3 ~/lxzbiotools/lxzbiotools/lxzbiotools.py  --help

 Usage: lxzbiotools.py [OPTIONS] COMMAND [ARGS]...

 Xingze Li's bioinformatics analysis scripts.
 emali: [e-mail]

╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --install-completion        [bash|zsh|fish|powershell|pwsh]  Install completion for the specified shell.        │
│                                                              [default: None]                                    │
│ --show-completion           [bash|zsh|fish|powershell|pwsh]  Show completion for the specified shell, to copy   │
│                                                              it or customize the installation.                  │
│                                                              [default: None]                                    │
│ --help                                                       Show this message and exit.                        │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ cds2pep         Convert cds file to pep file                                                                    │
│ excel2txt       Convert excel file to txt file                                                                  │
│ fa2fq           Convert a fasta file to a fastq file                                                            │
│ fq2fa           Convert a fastq file to a fasta file                                                            │
│ genstats        single or multiple genome information statistics                                                │
│ gfa2fa          Convert gfa file to fasta file                                                                  │
│ gff             Simplify gff3 file for WGD event analysis                                                       │
│ len             Get the length of each sequence                                                                 │
│ rds             Read a multi-FASTA file sequence and remove duplicates (by MD5 hash)                            │
│ run             Parallelized running tasks                                                                      │
│ seq             Extract sequences by sequence name or keyword                                                   │
│ tolf            Convert multi-line fasta to one-line fasta                                                      │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯