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Functions
ost.bindings.mmseqs2 Namespace Reference

Functions

def createdb
 
def create_index
 
def alignment
 

Function Documentation

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 57 of file mmseqs2.py.

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.

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.