From 3841d114fa7df6b5b2261ed2960301c7c5b3c5f2 Mon Sep 17 00:00:00 2001 From: Sean McKenzie Date: Mon, 6 Dec 2021 11:54:30 -0800 Subject: [PATCH] Added option to toggle ABCENTH full_pseudoexon_search if using ABCENTH as annotator --- HAPpy/__main__.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/HAPpy/__main__.py b/HAPpy/__main__.py index fd41941..973a1bf 100755 --- a/HAPpy/__main__.py +++ b/HAPpy/__main__.py @@ -817,6 +817,9 @@ def main(): the "--annotator ABCENTH" option.') addl_args.add_argument('--annotator', default = "genewise", help = 'Program to use for building final annotations. Currently the options \ are "genewise" (default) and "ABCENTH". I plan to add support for hint-guided AUGUSTUS at some point.') + run_args.add_argument('--ABCENTH_full_pseudoexon_search', default = True, help = 'Speficies whether ABCENTH should use genewise to \ + extend pseudogenized exon hits (default = True). Specifying "False" can substantially speed up ABCENTH on highly fragmented genome \ + at the expense of recovering slightly less sequence for pseudogenes (genes without frameshifts/internal stop codons are unaffected)') run_args.add_argument('--augustus_profile_dir', default = None, help = 'directory of augustus profiles corresponding to entries in "--hmm_dir" \ (for optional use with "--hmm_dir " and "--annotator augustus")') run_args.add_argument('--augustus_species', default = 'fly', help = 'species name for augustus parameters (default = "fly")') @@ -942,7 +945,7 @@ def main(): stdout = open(args.output_dir + '/abcenth_cluster_info.tsv','w')) subprocess.call(shlex.split('ABCENTH --genome ' + args.target_genome + ' --table ' + args.output_dir + '/abcenth_filtered_hit_table.tsv --query_exon_info_table ' + args.output_dir + - '/abcenth_cluster_info.tsv'), stdout = open(args.output_dir + '/ABCENTH.gtf','w')) + '/abcenth_cluster_info.tsv --full_pseudoexon_search ' + str(args.ABCENTH_full_pseudoexon_search)), stdout = open(args.output_dir + '/ABCENTH.gtf','w')) if 'genewise' in args.annotator: os.environ['WISECONFIGDIR'] = path_dict['program_dir'] + '/' + 'cfgFiles'