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added brackets to all callings of print for python 3 #14

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added brackets to all callings of print for python 3 #14

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67 changes: 36 additions & 31 deletions reago.py
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Original file line number Diff line number Diff line change
Expand Up @@ -718,18 +718,18 @@ def draw_graph(graph, filename):


def print_help_info():
print "-----------------------------------------------------"
print "Usage: python reago.py filename.fasta output_dir -l READ_LENGTH"
print "Optional parameters:"
print "-o OVERLAP, default 0.8"
print "-e ERROR_CORRECTION_THRESHOLD, default 0.05"
print "-t TIP_SIZE, default 30"
print "-b PATH_FINDING_PARAMETER, default 10"
print "Dependencies:"
print "1. Readjoiner 1.2"
print "2. Infernal 1.1.1"
print "-----------------------------------------------------"
sys.exit(1)
print ("-----------------------------------------------------")
print ("Usage: python reago.py filename.fasta output_dir -l READ_LENGTH")
print ("Optional parameters:")
print ("-o OVERLAP, default 0.8")
print ("-e ERROR_CORRECTION_THRESHOLD, default 0.05")
print ("-t TIP_SIZE, default 30")
print ("-b PATH_FINDING_PARAMETER, default 10")
print ("Dependencies:")
print ("1. Readjoiner 1.2")
print ("2. Infernal 1.1.1")
print ("-----------------------------------------------------")




Expand All @@ -745,33 +745,38 @@ def print_help_info():
args = sys.argv
if len(args) < 4:
print_help_info()
sys.exit(0)

filename = args[1]
output_dir = args[2]
if output_dir[-1] != "/":
output_dir += "/"

if os.path.exists(filename) == False:
print "Error: File", "\'" + filename + "\'", "doesn't exist."
print ("Error: File", "\'" + filename + "\'", "doesn't exist.")
print_help_info()
sys.exit(1)

for idx in range(3, len(args) - 1, 2):
arg, val = args[idx], float(args[idx+1])
if arg not in arg_range:
print "Error - Invalid arg:", arg
print ("Error - Invalid arg:", arg)
print_help_info()
sys.exit(1)

min_val, max_val = arg_range[arg][:2]
if val < min_val or val >= max_val:
print "Error: Invalid value for", arg
print "valid range:", "[" + str(min_val) + ", " + str(max_val) + ")"
print ("Error: Invalid value for", arg)
print ("valid range:", "[" + str(min_val) + ", " + str(max_val) + ")")
print_help_info()
sys.exit(1)
else:
arg_range[arg][2] = val

if arg_range["-l"][2] == None:
print "Error: read length is required"
print ("Error: read length is required")
print_help_info()
sys.exit(1)

MIN_OVERLAP = int(arg_range["-l"][2] * arg_range["-o"][2])
READ_LEN = int(arg_range["-l"][2])
Expand All @@ -788,7 +793,7 @@ def print_help_info():
fragments_path = output_dir + "fragments.fasta"

if os.path.exists(filename) == False:
print "Error: File", "\'" + filename + "\'", "doesn't exist."
print ("Error: File", "\'" + filename + "\'", "doesn't exist.")
sys.exit(1)

if os.path.exists(output_dir) == False:
Expand All @@ -799,24 +804,24 @@ def print_help_info():


##### main procedure starts
print timestamp(), "REAGO (v1.10) started..."
print "Input file:", filename
print "Parameters:"
print (timestamp(), "REAGO (v1.10) started...")
print ("Input file:", filename)
print ("Parameters:")
for arg in arg_range:
print arg, arg_range[arg][2]
print (arg, arg_range[arg][2])

print timestamp(), "Reading input file..."
print (timestamp(), "Reading input file...")
read_db, r_pos, cm_pos = get_fa(filename)
read_db_original = dict(read_db)
read_position_db = initialize_read_pos(read_db)
read_db = combine_duplicated_reads(read_db)


print timestamp(), "Initializing overlap graph..."
print (timestamp(), "Initializing overlap graph...")
G = create_graph_using_rj(read_db, "graph")
subgraphs = nx.weakly_connected_component_subgraphs(G)

print timestamp(), "Recovering 16S rRNAs..."
print (timestamp(), "Recovering 16S rRNAs...")
full_genes = []
scaffold_candidates = []
for subgraph in subgraphs:
Expand All @@ -838,16 +843,16 @@ def print_help_info():
full_genes += full
scaffold_candidates += scaf

print timestamp(), "Scaffolding on short 16S rRNA segments..."
print (timestamp(), "Scaffolding on short 16S rRNA segments...")
scaf, remaining = scaffold(scaffold_candidates)
full_genes += scaf

print timestamp(), "Write to Files..."
print (timestamp(), "Write to Files...")
write_gene(full_genes)
write_frag(remaining)


print timestamp(), "Done."
print "- Number of 16S rRNAs:", len(full_genes)
print "- Full genes:", full_genes_path
print "- Gene fragments:", fragments_path
print (timestamp(), "Done.")
print ("- Number of 16S rRNAs:", len(full_genes))
print ("- Full genes:", full_genes_path)
print ("- Gene fragments:", fragments_path)