pycdhit#

A Python interface for CD-HIT package.

Functions

read_fasta(file)

Parse file in fasta format.

write_fasta(file, data)

Write fasta data to a file.

read_clstr(file)

Parse file in clstr format.

cd_hit(**kwargs)

Run command cd-hit.

cd_hit_2d(**kwargs)

Run command cd-hit-2d.

cd_hit_est(**kwargs)

Run command cd-hit-est.

cd_hit_est_2d(**kwargs)

Run command cd-hit-est-2d.

cd_hit_div(**kwargs)

Run command cd-hit-div.

cd_hit_454(**kwargs)

Run command cd-hit-454.

cd_hit_dup(**kwargs)

Run command cd-hit-dup.

cd_hit_lap(**kwargs)

Run command cd-hit-lap.

Classes

CommandBase(prog[, path])

Base class for command-line programs.

CDHIT([prog, path])

Class for CD-HIT programs.
class CommandBase(prog: str, path: str | None = None)#

Base class for command-line programs.

Parameters:

  • prog – Name of the program.

  • path – Path of the program. Default None.

options#

Parameters and arguments.

Type:

dict

subprocess#

The finished process. Default None.

Type:

CompletedProcess

help()#

Print help message.

set_options(**kwargs) → CommandBase#

Set and update options and arguments.

Parameters:

**kwargs – Options and arguments of the command.

Returns:

Instance of self with options updated.

run()#

Run the program.

Returns:

The CompletedProcess.

class CDHIT(prog: str = 'cd-hit', path: str | None = None)#

Class for CD-HIT programs.

Parameters:

  • prog – Name of the program. {‘cd-hit’, ‘cd-hit-2d’, ‘cd-hit-est’, ‘cd-hit-est-2d’, ‘cd-hit-454’}, default ‘cd-hit’.

  • path – Path of the program. Default None.

options#

Parameters and arguments.

Type:

dict

subprocess#

The finished process. Default None.

Type:

CompletedProcess

help()#

Print help message.

set_options(**kwargs) → CDHIT#

Set and update options and arguments.

Parameters:

**kwargs – Options and arguments of the command.

Returns:

Instance of self with options updated.

cluster(input1: pandas.DataFrame, input2: pandas.DataFrame | None = None) → Tuple[pandas.DataFrame, ...]#

Run the program with DataFrame input.

Parameters:

  • input1 – Input fasta data.

  • input2 – Input fasta data. Required for 2D programs.

Returns:

The output fasta and clstr data, as tuple of DataFrame.

Note

Specifiy the option ‘o’ to keep the output files.

run()#

Run the program.

Returns:

The CompletedProcess.

read_fasta(file: str | Path) → pandas.DataFrame#

Parse file in fasta format.

Parameters:

file – A file path.

Returns:

The data of fasta file.

write_fasta(file: str | Path, data: pandas.DataFrame)#

Write fasta data to a file.

Parameters:

  • file – A file path.

  • data – A DataFrame with columns ‘identifier’ and ‘sequence’.

read_clstr(file: str | Path) → pandas.DataFrame#

Parse file in clstr format.

Parameters:

file – A file path.

Returns:

The data of clstr file.

cd_hit(**kwargs) → CompletedProcess#

Run command cd-hit.

If environment variable CD_HIT_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises:
cd_hit_2d(**kwargs) → CompletedProcess#

Run command cd-hit-2d.

If environment variable CD_HIT_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises:
cd_hit_est(**kwargs) → CompletedProcess#

Run command cd-hit-est.

If environment variable CD_HIT_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises:
cd_hit_est_2d(**kwargs) → CompletedProcess#

Run command cd-hit-est-2d.

If environment variable CD_HIT_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises:
cd_hit_div(**kwargs) → CompletedProcess#

Run command cd-hit-div.

If environment variable CD_HIT_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises:
cd_hit_454(**kwargs) → CompletedProcess#

Run command cd-hit-454.

If environment variable CD_HIT_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises:
cd_hit_dup(**kwargs) → CompletedProcess#

Run command cd-hit-dup.

If environment variable CD_HIT_AUXTOOLS_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises:
cd_hit_lap(**kwargs) → CompletedProcess#

Run command cd-hit-lap.

If environment variable CD_HIT_AUXTOOLS_DIR exists, it will be used as the path of the program.

Parameters:

**kwargs – Parameters and arguments of the command.

Returns:

The CompletedProcess.

Raises: