bed2idt

Installation

Via pip

$ pip install bed2idt 

CLI

Usage:

$ bed2idt [OPTIONS] COMMAND [ARGS]...

Options:

• --version
• --install-completion: Install completion for the current shell.
• --show-completion: Show completion for the current shell, to copy it or customize the installation.
• --help: Show this message and exit.

Commands:

• plates
• tubes

bed2idt plates

Usage:

$ bed2idt plates [OPTIONS] BEDFILE

Arguments:

• BEDFILE: The path to the bed file [required]

Options:

• --output FILE: The output location of the file. Defaults to output.xlsx [default: output.xlsx]
• --splitby [pool|ref|ref_pool|none]: Should the primers be split across different plate [default: pool]
• --fillby [rows|cols]: How should the plate be filled [default: cols]
• --plateprefix TEXT: The prefix used in naming sheets in the excel file [default: plate]
• --force / --no-force: Override the output directory
• --randomise / --no-randomise: Randomise the order of primers within a plate [default: no-randomise]
• --platesize [96|384]: The size of the plate to use [default: 96]
• --help: Show this message and exit.

bed2idt tubes

Usage:

$ bed2idt tubes [OPTIONS] BEDFILE

Arguments:

• BEDFILE: The path to the bed file [required]

Options:

• --output FILE: The output location of the file. Defaults to output.xlsx [default: output.xlsx]
• --scale [25nm|100nm|250nm|1um|5um|10um]: The concentration of the primers [default: 25nm]
• --purification [STD|PAGE|HPLC|IEHPLC|RNASE|DUALHPLC|PAGEHPLC]: The purification of the primers [default: STD]
• --force / --no-force: Override the output directory
• --help: Show this message and exit.