skimindex.unix.obitools

OBITools wrapper module using plumbum.

Provides Pythonic interfaces to OBITools commands installed in the image. All tools can be used with piping via plumbum's | operator.

Example

from skimindex.obitools import obiconvert, obigrep, obidistribute from plumbum import FG

(obiconvert["input.fasta", "-t", "fasta"] | obigrep["-s", "^count>10"] | obidistribute["-o", "output_{s}.fasta"]) & FG

obiconvert

obiconvert(*args) -> LoggedBoundCommand

Convert between different sequence file formats.

obiscript

obiscript(script_path: str, *args) -> LoggedBoundCommand

Execute an OBITools Lua script on sequence data.

obigrep

obigrep(*args) -> LoggedBoundCommand

Filter sequences based on various criteria.

obidistribute

obidistribute(*args) -> LoggedBoundCommand

Distribute sequences to multiple output files.

obisplit

obisplit(*args) -> LoggedBoundCommand

Split sequences into overlapping fragments.

obicount

obicount(*args) -> LoggedBoundCommand

Count occurrences of sequences.

obiuniq

obiuniq(*args) -> LoggedBoundCommand

Remove duplicate sequences.

obisummary

obisummary(*args) -> LoggedBoundCommand

Generate summary statistics for sequences.

obijoin

obijoin(*args) -> LoggedBoundCommand

Join sequence files.

obiclean

obiclean(*args) -> LoggedBoundCommand

Clean sequences (remove ambiguous bases, etc.).

obicomplement

obicomplement(*args) -> LoggedBoundCommand

Get complement/reverse complement of sequences.

obidemerge

obidemerge(*args) -> LoggedBoundCommand

Merge de-multiplexed sequences.

obimultiplex

obimultiplex(*args) -> LoggedBoundCommand

Demultiplex sequences by barcode.

obiconsensus

obiconsensus(*args) -> LoggedBoundCommand

Build consensus sequences.

obik

obik(*args) -> LoggedBoundCommand

Execute an obik command (count, filter, etc).

obik_count

obik_count(*args) -> LoggedBoundCommand

Count k-mers (obik count).

obik_filter

obik_filter(*args) -> LoggedBoundCommand

Filter by k-mers (obik filter).

obikindex

obikindex(*args) -> LoggedBoundCommand

Build k-mer index.

obikmerindex

obikmerindex(*args) -> LoggedBoundCommand

Build k-mer sequence index.

obikmermatch

obikmermatch(*args) -> LoggedBoundCommand

Match sequences against k-mer index.

obikmersimcount

obikmersimcount(*args) -> LoggedBoundCommand

Count k-mer similarity.

obipcr

obipcr(*args) -> LoggedBoundCommand

Simulate PCR with primers.

obitagpcr

obitagpcr(*args) -> LoggedBoundCommand

Tag sequences by PCR.

obimicrosat

obimicrosat(*args) -> LoggedBoundCommand

Analyze microsatellites.

obitaxonomy

obitaxonomy(*args) -> LoggedBoundCommand

Assign taxonomic information.

obitag

obitag(*args) -> LoggedBoundCommand

Tag sequences with metadata.

obilandmark

obilandmark(*args) -> LoggedBoundCommand

Find sequence landmarks.

obilowmask

obilowmask(*args) -> LoggedBoundCommand

Mask low-complexity regions.

obimatrix

obimatrix(*args) -> LoggedBoundCommand

Generate sequence matrices.

obicsv

obicsv(*args) -> LoggedBoundCommand

Export to CSV format.

obipairing

obipairing(*args) -> LoggedBoundCommand

Handle paired-end reads.

obiannotate

obiannotate(*args) -> LoggedBoundCommand

Annotate sequences.

obicleandb

obicleandb(*args) -> LoggedBoundCommand

Clean sequence database.

obisuperkmer

obisuperkmer(*args) -> LoggedBoundCommand

Work with super k-mers.

obilowermark

obilowermark(*args) -> LoggedBoundCommand

Mark lower case regions.

obirefidx

obirefidx(*args) -> LoggedBoundCommand

Build reference index.

obireffamidx

obireffamidx(*args) -> LoggedBoundCommand

Build reference family index.

help

help(tool_name: str) -> str

Return the --help output for an OBITools4 tool.

Parameters:

Name	Type	Description	Default
`tool_name`	`str`	OBITools4 executable name, e.g. `"obigrep"` or `"obiconvert"`.	required

Returns:

Type	Description
`str`	Help text string, or an error message if the tool is not found.