Command Line Interface

Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes.

Usage

usage: demultiplex [-h] [-v] {guess,demux,match} ...

Options

-v¶: show program's version number and exit

Sub-commands

guess

Retrieve the most frequent barcodes.

Usage

usage: __main__.py guess [-h] [-r] [--format {normal,x,umi,unknown}]
                         [-s START] [-e END] [-o OUTPUT] [-n SAMPLE_SIZE] [-f]
                         [-t THRESHOLD]
                         INPUT

Positional Arguments

input_handle INPUT¶

input file

Default: None
Type: _open
Required

Options

-r¶

extract the barcodes from the read

Default: False

--format¶

provdide the header format

Default: None
Choices: normal, x, umi, unknown

-s¶

start of the selection

Default: None
Type: int

-e¶

end of the selection

Default: None
Type: int

-o OUTPUT¶

output file

Default: -
Type: _open

-n¶

sample size

Default: 1000000
Type: int

-f¶

select on frequency instead of a fixed amount

Default: False

-t¶

threshold for the selection method

Default: 12
Type: int

demux

Demultiplex any number of files given a list of barcodes.

Usage

usage: __main__.py demux [-h] [-r] [--format {normal,x,umi,unknown}]
                         [-s START] [-e END] [-m MISMATCH] [-d] [-p PATH]
                         BARCODES INPUT [INPUT ...]

Positional Arguments

barcodes_handle BARCODES¶

barcodes file

Default: None
Type: _open
Required

input_handles INPUT¶

input files

Default: None
Type: _open
Required

Options

-r¶

extract the barcodes from the read

Default: False

--format¶

provdide the header format

Default: None
Choices: normal, x, umi, unknown

-s¶

start of the selection

Default: None
Type: int

-e¶

end of the selection

Default: None
Type: int

-m¶

number of mismatches

Default: 1
Type: int

-d¶

use Levenshtein distance

Default: False

-p¶

output directory

Default: .
Type: str

match

Demultiplex one file given a list of barcode tuples.

Usage

usage: __main__.py match [-h] [-m MISMATCH] [-d] [-p PATH] [-f] [-D]
                         BARCODES INPUT [INPUT ...]

Positional Arguments

barcodes_handle BARCODES¶

barcodes file

Default: None
Type: _open
Required

input_handles INPUT¶

input files

Default: None
Type: _open
Required

Options

-m¶

number of mismatches

Default: 1
Type: int

-d¶

use Levenshtein distance

Default: False

-p¶

output directory

Default: .
Type: str

-f¶

write multiple matches to separate files

Default: False

-D¶

directional input data

Default: False