Initialization of single-end dataset

assnake/api/fs_helpers.py

@@ -49,6 +49,32 @@ def get_samples_from_dir(directory_with_reads, modify_name = None):
             for s in samples
         ]
 
+    if len(samples_list) == 0:
+        ending_variant = {'name': 'single_end', 'strands': {'R1': '', 'R2':'_R2'}}
+        variant_w_ext = ending_variant['strands']['R1'] + ext
+        globbing_path = os.path.join(directory_with_reads, '*' + variant_w_ext)
+        files_mathching_pattern = glob.glob(globbing_path)
+
+        # get sample names
+        samples = [
+            filename.split('/')[-1].replace(variant_w_ext, '') # Take last part of path (basename) and replace _R1/fastq.gz with nothing to get sample name
+            for filename in files_mathching_pattern
+        ]
+
+        # prepare sample dicts
+        samples_list += [
+            {
+                'name_in_run': s,
+                'modified_name': modify_name(s) if modify_name is not None else s,
+
+                'ending_variant_id': ending_variant['name'],
+                'ending_variant_R1': ending_variant['strands']['R1'],
+                'ending_variant_R2': ending_variant['strands']['R2'],
+                'directory': directory_with_reads,
+                'extension': ext
+            } 
+            for s in samples
+        ]
 
     return pd.DataFrame(samples_list)
 
@@ -105,17 +131,20 @@ def create_links(import_dir, samples, hard = False, create_dir_if_not_exist = Fa
 
         if rename:
             os.rename(src_r1, dst_r1)
-            os.rename(src_r2, dst_r2)
+            if os.path.exists(src_r2):
+                os.rename(src_r2, dst_r2)
             return
 
         if hard:
             copy2(src_r1, dst_r1)
-            copy2(src_r2, dst_r2)
+            if os.path.exists(src_r2):
+                copy2(src_r2, dst_r2)
             return
 
         try:
             os.symlink(src_r1, dst_r1)
-            os.symlink(src_r2, dst_r2)
+            if os.path.exists(src_r2):
+                os.symlink(src_r2, dst_r2)
         except FileExistsError as e:
             print(e)
 

assnake/api/loaders.py

@@ -87,6 +87,16 @@ def load_sample(fs_prefix, df, preproc, df_sample,
                 if report_size:
                     size = os.path.getsize(r1) + os.path.getsize(r2)
                     sample_dict.update({'size': bytes2human(size, symbols='iec'), 'bytes': size})
+        elif os.path.isfile(r1):
+            containers.append(p)
+            if len(p) > len(final_preproc):
+                final_preproc = p
+                if report_size:
+                    size = os.path.getsize(r1) 
+                    sample_dict.update({'size': bytes2human(size, symbols='iec'), 'bytes': size})
+        else:
+            click.secho('There are no reads in a path: %s'%r1, fg='red')
+            exit()
     return {'df':df, 
             'df_sample':df_sample, 
             'df_sample':df_sample,  
@@ -108,7 +118,6 @@ def load_sample_set(wc_config, fs_prefix, df, preproc, samples_to_add = [], do_n
         do_not_add: list of sample names NOT to add
         pattern: sample names must match this glob pattern to be included. 
     '''
-
     if wc_config is None:
         wc_config = load_wc_config()
 

assnake/cli/assnake_cli.py

@@ -83,7 +83,7 @@ def dataset():
 dataset.add_command(dataset_commands.df_import_reads)
 dataset.add_command(dataset_commands.df_delete)
 dataset.add_command(dataset_commands.rescan_dataset)
-
+dataset.add_command(dataset_commands.df_update_info_wrapper)
 
 #---------------------------------------------------------------------------------------
 #                                  assnake  RESULT ***  group