Merge pull request #59 from adamklie/master

BUGFIX: TabixIterator does not have attribute .next(), added note in …

Author: lhqing

ALLCools/__main__.py

@@ -322,7 +322,7 @@ def merge_allc_register_subparser(subparser):
         "--output_path",
         type=str,
         required=True,
-        help="Path to the output merged ALLC file.",
+        help="Path to the output merged ALLC file (specify tsv.gz extension)",
     )
 
     parser_req.add_argument("--chrom_size_path", type=str, required=True, help=chrom_size_path_doc)

ALLCools/_merge_allc.py

@@ -40,7 +40,7 @@ def __init__(self, path, region):
             self.f_region = TabixIterator()
 
     def readline(self):
-        return next(self.f_region)
+        return self.f_region.__next__()
 
     def close(self):
         self.f.close()

ALLCools/count_matrix/dataset.py

@@ -94,7 +94,7 @@ def _determine_datasets(regions, quantifiers, chrom_size_path, tmp_dir):
                     "do not have index in its fourth column, adding it automatically. "
                     "If this is not desired, add a fourth column containing UNIQUE IDs to the BED file.",
                 )
-                region_bed_df[name] = (f"{name}_{i}" for i in range(region_bed_df.shape[0]))
+                region_bed_df[name] = [f"{name}_{i}" for i in range(region_bed_df.shape[0])]
             # check if name is unique()
             if region_bed_df.iloc[:, 3].duplicated().sum() > 0:
                 raise ValueError(f"Region IDs in {region_path} (fourth column) are not unique.")