diff --git a/PanACoTA/align_module/get_seqs.py b/PanACoTA/align_module/get_seqs.py index f9c79de4edd452a3b65e937c9e351cd639459335..d6d347daba06b74d1484408c7caf10bcf1c9e8e2 100755 --- a/PanACoTA/align_module/get_seqs.py +++ b/PanACoTA/align_module/get_seqs.py @@ -90,7 +90,7 @@ def get_all_seqs(all_genomes, dname, dbpath, listdir, aldir, all_fams, quiet): for genome in all_genomes: ge_gen = os.path.join(listdir, dname + "-getEntry_gen_" + genome + ".txt") ge_prt = os.path.join(listdir, dname + "-getEntry_prt_" + genome + ".txt") - logger.details("Extracting proteins and genes from {}".format(genome)) + logger.details(f"Extracting proteins and genes from {genome}") prtdb = os.path.join(dbpath, "Proteins", genome + ".prt") gendb = os.path.join(dbpath, "Genes", genome + ".gen") get_genome_seqs(prtdb, ge_prt, files_todo) @@ -254,7 +254,6 @@ def extract_sequences(to_extract, fasf, files_todo=None, outf=None): files_todo = frozenset(files_todo) if type(to_extract) == list: to_extract = frozenset(to_extract) - # State machine variables previous_fp = None