# HG changeset patch
# User public-health-bioinformatics
# Date 1646854868 0
# Node ID 42e34f1f61a1abc0ad035caac53ae1eff98709eb
# Parent  f5481e8b716dd64d77f68cb58e2f6ad59dbdf644
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 9c95d7322121c8a4d8f36adf8e0d821992cf9173-dirty"

diff -r f5481e8b716d -r 42e34f1f61a1 adjust_bracken_for_unclassified_reads.py
--- a/adjust_bracken_for_unclassified_reads.py	Mon Feb 28 23:29:01 2022 +0000
+++ b/adjust_bracken_for_unclassified_reads.py	Wed Mar 09 19:41:08 2022 +0000
@@ -17,7 +17,7 @@
             b['kraken_assigned_reads'] = int(row['kraken_assigned_reads'])
             b['added_reads'] = int(row['added_reads'])
             b['new_est_reads'] = int(row['new_est_reads'])
-            b['fraction_total_reads'] = float(row['fraction_total_reads'])
+            b['bracken_fraction_total_reads'] = float(row['fraction_total_reads'])
             bracken_abundances.append(b)
 
     return bracken_abundances
@@ -57,7 +57,8 @@
         'kraken_assigned_reads': kraken_report_unclassified_reads,
         'added_reads': 0,
         'new_est_reads': kraken_report_unclassified_reads,
-        'fraction_total_reads': percent_unclassified,
+        'kraken_fraction_total_reads': percent_unclassified,
+        'bracken_fraction_total_reads': 0.0,
     }
 
     bracken_abundances = [bracken_unclassified_entry] + bracken_abundances
@@ -69,15 +70,20 @@
         'kraken_assigned_reads',
         'added_reads',
         'new_est_reads',
-        'fraction_total_reads',
+        'total_reads',
+        'kraken_fraction_total_reads',
+        'bracken_fraction_total_reads',
     ]
 
     writer = csv.DictWriter(sys.stdout, fieldnames=output_fieldnames, dialect='excel-tab')
     writer.writeheader()
     
     for b in bracken_abundances:
-        adjusted_fraction_total_reads = float(b['new_est_reads']) / float(total_reads) 
-        b['fraction_total_reads'] = '{:.5f}'.format(adjusted_fraction_total_reads)
+        b['total_reads'] = total_reads
+        kraken_adjusted_fraction_total_reads = float(b['kraken_assigned_reads']) / float(total_reads)
+        b['kraken_fraction_total_reads'] = '{:.6f}'.format(kraken_adjusted_fraction_total_reads)
+        bracken_adjusted_fraction_total_reads = float(b['new_est_reads']) / float(total_reads)
+        b['bracken_fraction_total_reads'] = '{:.6f}'.format(bracken_adjusted_fraction_total_reads)
         writer.writerow(b)
     
 if __name__ == '__main__':