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fix max_output_edges
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@olga24912
olga24912 committed Jul 13, 2020
1 parent 9dc1fef commit 1ab078d
Showing 1 changed file with 11 additions and 11 deletions.
22 changes: 11 additions & 11 deletions sgtk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -331,23 +331,23 @@ 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"]:
prevdir = os.getcwd()
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"]:
prevdir = os.getcwd()
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)


Expand All @@ -356,23 +356,23 @@ 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"]:
prevdir = os.getcwd()
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"]:
prevdir = os.getcwd()
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)


Expand All @@ -381,39 +381,39 @@ 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"]:
prevdir = os.getcwd()
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"]:
prevdir = os.getcwd()
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"]:
prevdir = os.getcwd()
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"]:
prevdir = os.getcwd()
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
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