integrating bam stats

frangiPANe/generate_stats.py

@@ -194,8 +194,8 @@ def dashboard_group(df):
     # show the dashboard with the data embedded ,
     # (for using in an html download of the notebook so that
     # no 'callback' is required from the browser to get the data)
-    dashboard.embed()
-    #display(dashboard)
+    #dashboard.embed()
+    display(dashboard)
 
 def dashboard_fastq(csv, total_size, group_file, output_dir):
 
@@ -275,10 +275,8 @@ def dashboard_fastq(csv, total_size, group_file, output_dir):
     plt.savefig(os.path.join(output_dir,f"sample_reads_base_ratio.png"))
     plt.close()
 
-def dashboard_flagstat(stat_file, group_file, output_png):
+def dashboard_flagstat(stat_file, df_group, output_png):
 
-    id_dict,df_group = frangiPANe.read_group_file(group_file)
-    
     df_bam_stat = pd.read_csv(stat_file, index_col=False, sep=",")
     df_bam_stat.sort_values(by=['sample'], inplace=True)
 

frangiPANe/snakefiles/generate_jupyter_book.smk

@@ -3,7 +3,9 @@ rule generate_jupyter_book:
         jb_file=f"{ frangipane_obj.install_path }/report/frangiPANe_report.ipynb",
         ref_png=f"{frangipane_obj.path_stat_plot}/00_ref.png",
         ref_csv = f"{frangipane_obj.path_stat_sum}/00_ref.txt",
-        fastqstat_csv = rules.merge_fastq_stats.output.stat_file
+        fastqstat_csv = rules.merge_fastq_stats.output.stat_file,
+        bamstat_csv = rules.plot_mapping.input.csv,
+        bam_png = rules.plot_mapping.output.png_mapping
     output:
         jb_file=f"{ frangipane_obj.path_output }/report/frangiPANe_stats.ipynb"
     params:

frangiPANe/snakefiles/merge_flagstat.smk

@@ -34,7 +34,7 @@ rule merge_flagstat:
                 for line in stat:
                     line = line.rstrip()
 
-                    if 'mapped (' in line or 'paired (' in line or 'singleton' in line:
+                    if 'mapped (' in line or 'paired (' in line and not 'primary' in line or 'singleton' in line:
                         # print(line.split('(')[1].split('%')[0])
                         newLine += f",{line.split('(')[1].split('%')[0]}"
 

frangiPANe/snakemake_scripts/generate_jb_frangiPANe.py

@@ -16,7 +16,9 @@ dico = {
     "ref_png" : snakemake.input.ref_png,
     "ref_csv" : snakemake.input.ref_csv,
     "stat_file" : snakemake.input.fastq_csv,
-    "fastqstat_csv" : snakemake.input.fastqstat_csv
+    "fastqstat_csv" : snakemake.input.fastqstat_csv,
+    "bamstat_csv" : snakemake.input.bamstat.csv,
+    "bam_png" : snakemake.input.bam_png
     }
 
 with open(jb_input, "r", encoding="utf-8") as notebook_file: