new command: build_ref_db to build a reference database with metadata

for the taxonomic assignment of sequences

python/obitools3/commands/build_ref_db.pyx

@@ -0,0 +1,98 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms.dms cimport DMS
+from obitools3.dms.view import RollbackException
+from obitools3.dms.capi.build_reference_db cimport build_reference_db
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+from obitools3.dms.view.view cimport View
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+
+import sys
+
+
+__title__="Tag a set of sequences for PCR and sequencing errors identification"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+ 
+    group = parser.add_argument_group('obi build_ref_db specific options')
+
+    group.add_argument('--threshold','-t',
+                      action="store", dest="build_ref_db:threshold",
+                      metavar='<THRESHOLD>',
+                      default=0.0,
+                      type=float,
+                      help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.00"
+                           " (no threshold).")
+
+
+def run(config):
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi build_ref_db")
+
+    # Open the input: only the DMS
+    input = open_uri(config['obi']['inputURI'],
+                     dms_only=True)
+    if input is None:
+        raise Exception("Could not read input")
+    i_dms = input[0]
+    i_dms_name = input[0].name
+    i_view_name = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    final_o_view_name = output[1]
+    
+    # If the input and output DMS are not the same, build the database creating a temporary view that will be exported to 
+    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms:
+        temporary_view_name = final_o_view_name
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+    else:
+        o_view_name = final_o_view_name
+
+    # Read taxonomy name
+    taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
+
+    # Save command config in View comments
+    command_line = " ".join(sys.argv[1:])
+    comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
+
+    if build_reference_db(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
+        raise Exception("Error building a reference database")
+    
+    # If the input and output DMS are not the same, export result view to output DMS
+    if i_dms != o_dms:
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+    
+    # Save command config in DMS comments
+    o_dms.record_command_line(command_line)
+
+    print("\n")
+    print(repr(o_dms[final_o_view_name]))
+
+    # If the input and the output DMS are different, delete the temporary result view in the input DMS
+    if i_dms != o_dms:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    
+    i_dms.close()

python/obitools3/dms/dms.cfiles

@@ -1,5 +1,6 @@
 ../../../src/array_indexer.c
 ../../../src/bloom.c
+../../../src/build_reference_db.c
 ../../../src/char_str_indexer.c
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.c

python/obitools3/utils.cfiles

@@ -1,5 +1,6 @@
 ../../src/array_indexer.c
 ../../src/bloom.c
+../../src/build_reference_db.c
 ../../src/char_str_indexer.c
 ../../src/crc64.c
 ../../src/dna_seq_indexer.c