ost.bindings.mmseqs2 Namespace Reference

Functions
def	createdb (infasta, resultDB, exe_path=None)
def	create_index (trg_db, exe_path=None, directory=None)
def	alignment (query_db, trg_db, resultDB, directory, resultDB_m8, sen=None, exe_path=None, start_sens=None, sens_steps=None, fmt=None)

Function Documentation

alignment()

def ost.bindings.mmseqs2.alignment	(		query_db,
			trg_db,
			resultDB,
			directory,
			resultDB_m8,
			sen = None,
			exe_path = None,
			start_sens = None,
			sens_steps = None,
			fmt = None
	)

The alignment consists of two steps the prefilter and alignment.

:param query_db: The query database mmseqs2 file.
 (You need to initially convert a fasta file into a mmseqs2 database using createdb).
:type query_db: :class:`string`

:param trg_db: The target database mmseqs2 file.
 (You need to initially convert a fasta file into a mmseqs2 database using createdb).
:type trg_db: :class:`string`

:param resultDB: The output location.
 (Output of createdb)
:type resultDB: :class:`string`  

:param exe_path: The path where mmseqs2 executable is located.
:type exe_path: :class:`string`

:param directory: The directory for temperary files.
:type directory: :class:`string`

:param sen: It controls the speed and sensitivity of the search.
            A very fast search would use a sensitivity of 1.0,
            while a very sensitive search would use a sensitivity of up to 7.0.  
:type sen: :class:`float`

:param start_sens: Best hit fast. The lowest sensitivity is defined with --start-sens.                      
:type start_sens: :class:`int`

:param sens_steps: Best hit fast. 
       The number of steps to reach the highest sensitivity can be defined with --sens-steps.
:type sens_steps: :class:`int`

Convert the result database into a BLAST tab formatted file.
The file is formatted as a tab-separated list with 12 columns: 
(1,2) identifiers for query and target sequences/profiles, 
(3) sequence identity, 
(4) alignment length, 
(5) number of mismatches, 
(6) number of gap openings,
(7-8, 9-10) domain start and end-position in query and in target, 
(11) E-value, 
and (12) bit score.

The option --format-output defines a custom output format. 
The fields that are supported can be found in the following link:
https://github.com/soedinglab/mmseqs2/wiki#custom-alignment-format-with-convertalis

:param resultDB_m8: The output location
:type resultDB_m8: :class:`string`

:param fmt: Format output type, if the default is not used.
:type fmt: :class:`string`

Definition at line 56 of file mmseqs2.py.

create_index()

def ost.bindings.mmseqs2.create_index	(		trg_db,
			exe_path = None,
			directory = None
	)

An index file of the targetDB is computed for a fast read-in.
It is recommended to compute the index if the targetDB is reused for several searches.   
A directory for temporary files is generated. 
It is recommended to create this temporary folder on a local drive. 

:param trg_db: The target database mmseqs2 file.
 (You need to initially convert a fasta file into a mmseqs2 database using createdb).
:type trg_db: :class:`string`

:param exe_path: The path where mmseqs2 executable is located.
:type exe_path: :class:`string'

:param directory: The directory for temperary files.
:type directory: :class:`string`

Definition at line 28 of file mmseqs2.py.

createdb()

def ost.bindings.mmseqs2.createdb	(		infasta,
			resultDB,
			exe_path = None
	)

Convert fasta files containing query and/or target sequences into a mmseqs2 database.

:param infasta: The fasta file from which the mmseqs2 database will be created.
:type infasta: :class:`string`

:param resultDB: The output location for mmseqs2 database.
:type resultDB: :class:`string`  

:param exe_path: The path where mmseqs2 executable is located
:type exe_path: :class:`string`

Definition at line 5 of file mmseqs2.py.