From e3b8db9c75f553ab3aaab0848961f8f654e43b03 Mon Sep 17 00:00:00 2001 From: eeaunin Date: Wed, 7 Aug 2024 14:09:12 +0100 Subject: [PATCH] ran linting with black --- bin/autofilter.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/bin/autofilter.py b/bin/autofilter.py index d843308..8c1dc4e 100755 --- a/bin/autofilter.py +++ b/bin/autofilter.py @@ -42,9 +42,9 @@ def parse_args(): help="Path to the assembly_autofiltered.fasta file", default="autofiltered.fasta", ) - #parser.add_argument( + # parser.add_argument( # "-c", "--fcs_gx_and_tiara_summary", type=str, help="Path to the fcs-gx_and_tiara_combined_summary.csv file" - #) + # ) parser.add_argument( "-r", "--rejected_seq", @@ -57,7 +57,11 @@ def parse_args(): "-n", "--ncbi_rankedlineage_path", type=str, help="Path to the rankedlineage.dmp of NCBI taxonomy" ) parser.add_argument( - "--tiara_action_mode", type=str, choices=["warn", "remove"], default="warn", help="Action when Tiara detects a putative contaminant that is not reported as a contaminant by FCS-GX. The choices are 'warn' (print a warning) or 'remove' (remove this sequence from the assembly). Default: warn" + "--tiara_action_mode", + type=str, + choices=["warn", "remove"], + default="warn", + help="Action when Tiara detects a putative contaminant that is not reported as a contaminant by FCS-GX. The choices are 'warn' (print a warning) or 'remove' (remove this sequence from the assembly). Default: warn", ) parser.add_argument("-v", "--version", action="version", version=VERSION) return parser.parse_args() @@ -182,7 +186,7 @@ def main(): tiara_results_path = args.tiara fcs_gx_summary_path = args.fcsgx_summary filtered_assembly_path = args.output_auto_filtered - #combined_summary = args.fcs_gx_and_tiara_summary + # combined_summary = args.fcs_gx_and_tiara_summary excluded_seq_list_path = args.rejected_seq ncbi_rankedlist = args.ncbi_rankedlineage_path @@ -238,4 +242,4 @@ def main(): if __name__ == "__main__": - main() \ No newline at end of file + main()