Initial version of mmseqs2 binding

modules/bindings/pymod/CMakeLists.txt

@@ -15,6 +15,7 @@ blast.py
 cadscore.py
 kclust.py
 ialign.py
+mmseqs2.py
 )
 
 set(OST_BINDINGS_PYMOD_SOURCES

modules/bindings/pymod/mmseqs2.py

+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)