output change

metagenomics/bins_summary.py

@@ -15,14 +15,14 @@ def parse_options():
   input_group.add_argument("-d","--bin_depths",  dest="bin_depths",    help="MetaBAT2 aggregateDepths file", required=True, metavar="")
   input_group.add_argument("-B","--busco_dir",   dest="busco_dir",     help="Folder with BUSCO reports", required=False,  metavar="")
   input_group.add_argument("-c","--checkm",      dest="checkm_report", help="Checkm report file", required=False,  metavar="")
-  input_group.add_argument("-o","--output_file", dest="output_file",   help="Output name", required=True,  metavar="")
+  input_group.add_argument("-o","--output", dest="output_name",   help="Output base name", required=True,  metavar="")
 
   inputs = parser.parse_args()
   return inputs
 
-def bin_stats(bin_dir,output_file):
+def bin_stats(bin_dir,output_name):
   # File containing which contigs belongs to which bin.
-  bin_contigs_file = open("binContigs.tsv","w")
+  bin_contigs_file = open(output_name+"_binContigs.tsv","w")
 
   bin_file_list = os.listdir(bin_dir)  
   for bin in bin_file_list:
@@ -102,13 +102,13 @@ def main(argv):
   df = pd.DataFrame(columns=out_columns, index=bin_file_list)
 
   # Fill dataframe (df) with the input files data.
-  bin_stats(inputs.bin_dir, inputs.output_file)
+  bin_stats(inputs.bin_dir, inputs.output_name)
   bin_depths(inputs.bin_depths)
   read_checkm_report(inputs.checkm_report)
 
   read_busco(inputs.busco_dir)
   df.index.name = "Bin"
-  df.to_csv(inputs.output_file, sep="\t")
+  df.to_csv(inputs.output_name+"_bins_summary.tsv", sep="\t")
 
 
 if __name__ == "__main__":