From d994bf77349cdcb8a2c75d0475105a8dc87afa67 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Tue, 1 Dec 2020 10:24:29 +0100 Subject: [PATCH] remove obsolete function --- .../annotate_module/general_format_functions.py | 16 ---------------- test/test_unit/test_annotate/test_format_func.py | 11 ----------- 2 files changed, 27 deletions(-) diff --git a/PanACoTA/annotate_module/general_format_functions.py b/PanACoTA/annotate_module/general_format_functions.py index 0532b0a5..1659c6cb 100644 --- a/PanACoTA/annotate_module/general_format_functions.py +++ b/PanACoTA/annotate_module/general_format_functions.py @@ -281,19 +281,3 @@ def write_header(lstline, outfile): size = int(end) - int(start) + 1 towrite = " ".join([name, str(size), gene_name, info]) outfile.write(">" + towrite + "\n") - - -def get_contig_name(genome, cont_num): - """ - From a genome name and a contig number, write the header corresponding to this contig - (for 'Replicons' files) - - Parameters - ---------- - genome : str - genome name - cont_num : int - contig number - """ - return ">{}.{}".format(genome, str(cont_num).zfill(4)) - diff --git a/test/test_unit/test_annotate/test_format_func.py b/test/test_unit/test_annotate/test_format_func.py index 7f652f5e..9a0f779c 100755 --- a/test/test_unit/test_annotate/test_format_func.py +++ b/test/test_unit/test_annotate/test_format_func.py @@ -97,17 +97,6 @@ def test_write_gene(): assert tutil.compare_order_content(exp_file, lstfile) -def test_contig_name(): - """ - test that when we give a genome name and a contig number, it returns the expected fasta header - for Replicon files (no gene number) - """ - genome = "ESCO.1218.00005" - cont_num = 30 - head_line = ffunc.get_contig_name(genome, cont_num) - assert head_line == ">ESCO.1218.00005.0030" - - def test_write_header_gene(): """ From a given line of lstinfo file, giving info for a gene (start, end, gene name, -- GitLab