Converts primer.bed files to IDT ordering templates
Project description
bed2idt
This command-line interface (CLI) generates IDT input files from a 7-column primer bed file.
Description
The IDT Input File Generator CLI allows you to convert a primer bed file into IDT input files. IDT (Integrated DNA Technologies) is a company that provides custom DNA synthesis services. This tool automates the process of generating input files for ordering primers from IDT.
Installation
From pip
pip instal bed2idt
From Poetry / source
git clone https://github.com/ChrisgKent/bed2idt
poetry install && poetry build
Usage
To use the CLI, run the following command:
bed2idt [options] [command] [command-options]
Options
The CLI supports the following options:
-b, --bedfile
: Path to the primer bed file (required).-o, --output
: The output location for the generated IDT input file(s) (default:output.xlsx
).plate
command:-s, --splitby
: Specifies whether the primers should be split across more than one plate. Valid options arepool
,ref
,none
,(default:nest
pool
).-f, --fillby
: Specifies how the plates should be filled. Valid options arerows
orcols
(default:cols
).--plateprefix
: The prefix for the plate names
tube
command:-s, --scale
: The concentration of the primers. Valid options are25nm
,100nm
,250nm
,1um
,2um
,5um
,10um
,4nmU
,20nmU
,PU
, or25nmS
(default:25nm
).-p, --purification
: The purification method for the primers. Valid options areSTD
,PAGE
,HPLC
,IEHPLC
,RNASE
,DUALHPLC
, orPAGEHPLC
(default:STD
).
--force
: Overrides the output directory if it already exists.
Examples
-
Generate 96-well plate IDT input files for a primer bed file named
primer.bed
and save/overide the output asoutput.xlsx
, split by pools:bed2idt -b primer.bed --force plate --splitby pools
-
Generate tube IDT input files for a primer bed file named
primer.bed
, save the output ascustom_output.xlsx
, and specify a purification method:bed2idt -b primer.bed -o custom_output.xlsx tube --purification PAGE
-
Generate IDT input files for a primer bed file named
primer.bed
without splitting the primers across multiple plates:bed2idt -b primer.bed plate --splitby none
-
Generate IDT input files
primer.xlsx
for a primer.bed file namedprimer.bed
, splitting the plate by pool, and filling plates by col:bed2idt -b primer.bed -o primer.xlsx plate --splitby pools --filllby cols
Note: Make sure to replace python
with the appropriate command for running Python on your system.
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.