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import subprocess
import ost
from ost import settings
def 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`
"""
mmseqs2_exe = settings.Locate('mmseqs2', explicit_file_name=exe_path)
args=[mmseqs2_exe, 'createdb', infasta, resultDB]
ost.LogInfo(f"running MMseqs2 {' '.join(args)}")
mmseqs2_pipe=subprocess.run(args)
def 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`
"""
mmseqs2_exe = settings.Locate('mmseqs2', explicit_file_name=exe_path)
args=[mmseqs2_exe, 'createindex', trg_db, directory]
ost.LogInfo(f"running MMseqs2 {' '.join(args)}")
mmseqs2_pipe=subprocess.run(args)
def 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`
"""
mmseqs2_exe = settings.Locate('mmseqs2', explicit_file_name=exe_path)
command=[mmseqs2_exe, 'search', query_db, trg_db, resultDB, directory, '-a']
if sen:
sen=str(sen)
command.append('-s')
command.append(sen)
if start_sens and sens_steps:
start_sens=str(start_sens)
command.append('--start-sens')
command.append(start_sens)
sens_steps=str(sens_steps)
command.append('--sens-steps')
command.append(sens_steps)
ost.LogInfo(f"running MMseqs2 {' '.join(command)}")
mmseqs2_pipe=subprocess.run(command)
args=[mmseqs2_exe, 'convertalis', query_db, trg_db, resultDB, resultDB_m8]
if fmt:
args.append('--format-output')
args.append(fmt)
ost.LogInfo(f"running MMseqs2 (' '.join(args))")
mmseqs2_pipe=subprocess.run(args)
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