add script to convert to excel

bin/bactopia-teton

@@ -1,5 +1,5 @@
 #! /bin/bash
-VERSION=1.0.3
+VERSION=1.0.4
 PREFIX=$1
 
 # If no user input, print usage

bin/bracken-to-excel.py

@@ -0,0 +1,61 @@
+#! /usr/bin/env python3
+"""
+bracken-to-excel.py
+"""
+PROGRAM = "bracken-to-excel"
+VERSION = "2.2.2"
+import sys
+
+if __name__ == '__main__':
+    import argparse as ap
+    import pandas as pd
+
+    parser = ap.ArgumentParser(
+        prog=PROGRAM,
+        conflict_handler='resolve',
+        description=(
+            f'{PROGRAM} (v{VERSION}) - Write Bracken abundances to an Excel file'
+        )
+    )
+
+    parser.add_argument('prefix', metavar="PREFIX", type=str,
+                        help='Prefix to use for output files')
+    parser.add_argument('bracken_abundances', metavar="BRACKEN_ABUNDANCES", type=str,
+                        help='The merged Bracken output with abundances')
+    parser.add_argument('--limit', metavar='INT', type=int, default=5,
+                        help='Limit the result to the top N rows.')
+    parser.add_argument(
+        '--include_unclassified', action='store_true',
+        help='Include results for unclassified reads.'
+    )
+    parser.add_argument('--version', action='version',
+                        version=f'{PROGRAM} {VERSION}')
+
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(0)
+
+    args = parser.parse_args()
+
+    """
+    Read Bracken abundances
+    name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
+    Pseudomonas aeruginosa	287	S	591369	1309432	1900801	0.96175
+    Pseudomonas sp. Y5-11	2749808	S	11682	14249	25931	0.01312
+    Stutzerimonas stutzeri	316	S	5810	1135	6945	0.00351
+    """
+    bracken = pd.read_csv(args.bracken_abundances, sep='\t')
+    samples = bracken["sample"].unique()
+
+    # Write Excel file, with each sample getting its own sheet
+    with pd.ExcelWriter(f"{args.prefix}.xlsx") as writer:  
+        for sample in samples:
+            sheet_name = sample
+            if len(sample) > 31:
+                sheet_name = sample[:31]
+            df = bracken[bracken["sample"] == sample]
+            if not args.include_unclassified:
+                df = df[df["name"] != "unclassified"]
+
+            df.sort_values(by='fraction_total_reads', ascending=False).head(args.limit).to_excel(writer, sheet_name=sheet_name, index=False)
+            print(sample)