added default keyword arguments

README.md

@@ -165,7 +165,7 @@ Further, a second table (labeled as ```*_flanks.txt```) containing information r
 *  3' Flanking Sequence Bracketed Notation
 *  Potential Issues (such as: Possible indel or partial sequence)
 
-The ```Potential Issues``` column in this report is to draw attention to potential problem sequences (due to perhaps an indel or partial sequence) and requires the attention of the user to further evaluate the sequence for it's authenticity.  
+The ```Potential Issues``` column in this report is to draw attention to potential problem sequences (due to perhaps an indel or partial sequence) and requires the attention of the user to further evaluate the sequence for its authenticity.  
 
 Individual marker plots displaying reads vs. CE allele are created in PDF format. They are stored in the ```MarkerPlots/``` directory of the working directory:   
 * The first page of the PDF file contains the marker plots using a custom y-axis scale (i.e. the y-axis is scaled for each individual marker).  

lusSTR/wrappers/convert.py

@@ -175,19 +175,19 @@ def sort_table(table):
     return sorted_table
 
 
-def marker_plots(df, output_name, sex):
+def marker_plots(df, output_name, sex=False):
     Path("MarkerPlots").mkdir(parents=True, exist_ok=True)
     df["CE_Allele"] = df["CE_Allele"].astype(float)
     for id in df["SampleID"].unique():
         sample_id = f"{id}_sexchr" if sex else id
         with PdfPages(f"MarkerPlots/{output_name}_{sample_id}_marker_plots.pdf") as pdf:
-            make_plot(df, id, sex, False)
+            make_plot(df, id, sex, sameyaxis=False)
             pdf.savefig()
-            make_plot(df, id, sex, True)
+            make_plot(df, id, sex)
             pdf.savefig()
 
 
-def make_plot(df, id, sex, sameyaxis):
+def make_plot(df, id, sex=False, sameyaxis=True):
     sample_df = df[df["SampleID"] == id]
     sample_id = f"{id}_sexchr" if sex else id
     max_reads = max(sample_df["Reads"])
@@ -238,7 +238,7 @@ def main(input, out, kit, uas, sex, nocombine):
                 sex_final_table.to_csv(f"{output_name}_sexloci.txt", sep="\t", index=False)
         else:
             sex_final_table.to_csv(f"{output_name}_sexloci.txt", sep="\t", index=False)
-        marker_plots(sex_final_table, output_name, True)
+        marker_plots(sex_final_table, output_name, sex=True)
     if not uas:
         if not autosomal_final_table.empty:
             autosomal_flank_table.to_csv(f"{output_name}_flanks.txt", sep="\t", index=False)
@@ -250,7 +250,7 @@ def main(input, out, kit, uas, sex, nocombine):
             autosomal_final_table.to_csv(out, sep="\t", index=False)
     else:
         autosomal_final_table.to_csv(out, sep="\t", index=False)
-    marker_plots(autosomal_final_table, output_name, False)
+    marker_plots(autosomal_final_table, output_name)
 
 
 if __name__ == "__main__":