From 1ab078d4c33e29143ee7c699420f300e8836cec5 Mon Sep 17 00:00:00 2001 From: Olga Kunyavskaya Date: Mon, 13 Jul 2020 18:02:17 +0300 Subject: [PATCH] fix max_output_edges --- sgtk.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/sgtk.py b/sgtk.py index 044264e..0a13d6d 100755 --- a/sgtk.py +++ b/sgtk.py @@ -331,7 +331,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp DNA_PAIR_FR dna1.sam dna2.sam " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp DNA_PAIR_FR dna1.sam dna2.sam " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["rf"]: @@ -339,7 +339,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp DNA_PAIR_RF dna1.sam dna2.sam " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp DNA_PAIR_RF dna1.sam dna2.sam " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["ff"]: @@ -347,7 +347,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp DNA_PAIR_FF dna1.sam dna2.sam " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp DNA_PAIR_FF dna1.sam dna2.sam " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) @@ -356,7 +356,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp DNA_PAIR_FR " + lib.path[0] + " " + lib.path[1] + " " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp DNA_PAIR_FR " + lib.path[0] + " " + lib.path[1] + " " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["rfsam"]: @@ -364,7 +364,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp DNA_PAIR_RF " + lib.path[0] + " " + lib.path[1] + " " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp DNA_PAIR_RF " + lib.path[0] + " " + lib.path[1] + " " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["ffsam"]: @@ -372,7 +372,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp DNA_PAIR_FF " + lib.path[0] + " " + lib.path[1] + " " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp DNA_PAIR_FF " + lib.path[0] + " " + lib.path[1] + " " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) @@ -381,7 +381,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp LONG out.paf " + contig_file_name + " " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp LONG out.paf " + contig_file_name + " " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["scg"]: @@ -389,7 +389,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp CONNECTION " + lib.path[0] + " " + contig_file_name + " " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp CONNECTION " + lib.path[0] + " " + contig_file_name + " " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["fastg"]: @@ -397,7 +397,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp FASTG " + lib.path[0] + " " + contig_file_name + " " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp FASTG " + lib.path[0] + " " + contig_file_name + " " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["gfa"]: @@ -405,7 +405,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp GFA " + lib.path[0] + " " + lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp GFA " + lib.path[0] + " " + lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) for lib in args.libs["gfa2"]: @@ -413,7 +413,7 @@ def build_graph(contig_file_name, args): log.log("START BUILD GRAPH: " + lib.label) lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/") os.chdir(lib_dir) - os.system(path_to_exec_dir + "buildApp GFA2 " + lib.path[0] + " " + contig_file_name + " "+ lib.label + " " + args.max_output_edges) + os.system(path_to_exec_dir + "buildApp GFA2 " + lib.path[0] + " " + contig_file_name + " "+ lib.label + " " + str(args.max_output_edges)) os.chdir(prevdir) return