Batch type coerce and r2 file check

edilytics · Feb 16, 2022 · f917366 · f917366
1 parent 442a48c
commit f917366
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py
@@ -174,6 +174,11 @@ def main():
         #pandas either allows for auto-detect sep or for comment. not both
 #        batch_params=pd.read_csv(args.batch_settings,sep=None,engine='python',error_bad_lines=False)
         batch_params.columns = batch_params.columns.str.strip(' -\xd0')
+        int_columns = ['default_min_aln_score', 'min_average_read_quality', 'min_single_bp_quality', 'min_bp_quality_or_N',
+                       'quantification_window_size', 'quantification_window_center', 'exclude_bp_from_left', 'exclude_bp_from_right',
+                       'plot_window_size', 'max_rows_alleles_around_cut_to_plot']
+        for int_col in int_columns:
+            batch_params[int_col]=batch_params[int_col].astype(int)
 
         #rename column "a" to "amplicon_seq", etc
         batch_params.rename(index=str, columns=CRISPRessoShared.get_crispresso_options_lookup(), inplace=True)
@@ -215,7 +220,7 @@ def main():
                 else:
                     CRISPRessoShared.check_file(row.fastq_r1)
 
-            if 'fastq_r2' in row and row.fastq_r2 != "":
+            if 'fastq_r2' in row and row.fastq_r2 != "" and row.fastq_r2 != "nan":
                 CRISPRessoShared.check_file(row.fastq_r2)
 
             if 'input_bam' in row: