Add rename depth column

bin/quantification_by_contig_lineage.py

@@ -27,6 +27,7 @@ try:
     import re
     import sys
     import pandas as pd
+    import os
     from datetime import datetime
 except ImportError as error:
     print(error)
@@ -58,26 +59,27 @@ with open(args.list_of_input_files) as finput_list:
 
 # Merge results for all samples by lineage.
 for (sample_idx,sample_path) in enumerate(sample_files):
-    print(sample_idx)
+    print("Read " + sample_path)
     if(sample_idx==0):
         merge  = pd.read_csv(sample_path, delimiter='\t', dtype=str)
-        sample_name = sample_path
-        if('consensus_tax_id' in merge.columns): merge.drop('consensus_tax_id', inplace=True, axis=1)
+        sample_name = os.path.splitext(sample_path)[0]
     else:
         sample_results = pd.read_csv(sample_path, delimiter='\t', dtype=str)
         merge = pd.merge(merge,sample_results,left_on=["tax_id_by_level","lineage_by_level"],right_on=["tax_id_by_level","lineage_by_level"], how='outer', suffixes=('_' + sample_name,''))
-        sample_name = sample_path
-        if('consensus_tax_id' in merge.columns): merge.drop('consensus_tax_id', inplace=True, axis=1)
+        print (merge.head())
+        sample_name = os.path.splitext(sample_path)[0]
+    if('consensus_tax_id' in merge.columns): merge.drop('consensus_tax_id', inplace=True, axis=1)
 
 # Rename columns corresponding to the last sample file.
-sample_name = sample_path
+sample_name = os.path.splitext(sample_path)[0]
 
 merge.rename(columns = {'name_contigs': 'name_contigs_' + sample_name, \
 'nb_contigs': 'nb_contigs_' + sample_name,\
-'nb_reads': 'nb_reads_' + sample_name},inplace=True)
+'nb_reads': 'nb_reads_' + sample_name,\
+'depth': 'depth_' + sample_name},inplace=True)
 
 # Fill the NaN by 0.
 merge.fillna(0, inplace=True)
-
+print("Write " + args.output_file)
 # Write merge data frame in output file.
 merge.to_csv(args.output_file, sep="\t", index=False)