From 7300e702bb8137c691d880eb979d6bd1a1140b39 Mon Sep 17 00:00:00 2001 From: bart <bart.nijsse@wur.nl> Date: Thu, 30 Jun 2022 18:11:44 +0200 Subject: [PATCH] output change --- metagenomics/bins_summary.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/metagenomics/bins_summary.py b/metagenomics/bins_summary.py index a34ddb5..016163b 100644 --- a/metagenomics/bins_summary.py +++ b/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__": -- GitLab