Fixed a bug where some commands wouldn't work if the input DMS was not

in the current directory

python/obitools3/commands/align.pyx

@@ -229,7 +229,7 @@ def run(config):
     
     # Call cython alignment function
       # Using default ID columns of the view. TODO discuss adding option
-    align_columns(i_dms_name,  \
+    align_columns(i_dms.full_path,  \
                   i_view_name,  \
                   o_view_name,  \
                   input_view_2_n   = i_view_name_2,  \

python/obitools3/commands/build_ref_db.pyx

@@ -81,7 +81,7 @@ def run(config):
     input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_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:
+    if build_reference_db(i_dms.full_path, 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

python/obitools3/commands/clean.pyx

@@ -107,7 +107,7 @@ def run(config):
     command_line = " ".join(sys.argv[1:])
     comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
 
-    if obi_clean(tobytes(i_dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
+    if obi_clean(i_dms.full_path, tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
               config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
         raise Exception("Error running obiclean")
     

python/obitools3/commands/ecopcr.pyx

@@ -178,8 +178,8 @@ def run(config):
 
     # TODO: primers in comments?
 
-    if obi_ecopcr(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), \
-                  tobytes(o_dms_name), tobytes(o_view_name), comments, \
+    if obi_ecopcr(i_dms.full_path, tobytes(i_view_name), tobytes(taxonomy_name), \
+                  o_dms.full_path, tobytes(o_view_name), comments, \
                   tobytes(config['ecopcr']['primer1']), tobytes(config['ecopcr']['primer2']), \
                   config['ecopcr']['error'], \
                   config['ecopcr']['min-length'], config['ecopcr']['max-length'], \

python/obitools3/commands/ecotag.pyx

@@ -101,7 +101,7 @@ def run(config):
     input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     comments = View.print_config(config, "ecotag", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
 
-    if obi_ecotag(tobytes(i_dms_name), tobytes(i_view_name), \
+    if obi_ecotag(i_dms.full_path, tobytes(i_view_name), \
                   tobytes(ref_dms_name), tobytes(ref_view_name), \
                   tobytes(taxo_dms_name), tobytes(taxonomy_name), \
                   tobytes(o_view_name), comments,