Fix batch mode pandas warning. (#70) (#429)

* refactor to call method on DataFrame, rather than Series.
Removes warning.

* Fix pandas future warning in CRISPRessoWGS

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Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com>

CRISPResso2/CRISPRessoBatchCORE.py

@@ -196,7 +196,7 @@ def main():
                 batch_params[arg] = getattr(args, arg)
             else:
                 if (getattr(args, arg) is not None):
-                    batch_params[arg].fillna(value=getattr(args, arg), inplace=True)
+                    batch_params.fillna(value={arg: getattr(args, arg)}, inplace=True)
 
         # assert that all names are unique
         # and clean names

CRISPResso2/CRISPRessoWGSCORE.py

@@ -582,7 +582,7 @@ def set_filenames(row):
             cols_to_print = ["chr_id", "bpstart", "bpend", "sgRNA", "Expected_HDR", "Coding_sequence", "sequence", "n_reads", "bam_file_with_reads_in_region", "fastq_file_trimmed_reads_in_region"]
             if args.gene_annotations:
                 cols_to_print.append('gene_overlapping')
-            df_regions.fillna('NA').to_csv(report_reads_aligned_filename, sep='\t', columns = cols_to_print, index_label="Name")
+            df_regions.infer_objects(copy=False).fillna('NA').to_csv(report_reads_aligned_filename, sep='\t', columns = cols_to_print, index_label="Name")
 
             #save progress
             crispresso2_info['running_info']['finished_steps']['generation_of_fastq_files_for_each_amplicon'] = True