comparison tools/protein_analysis/promoter2.py @ 8:976a5f2833cd draft

Uploaded v0.1.1 of the bundle, which fixes an error in the header of the tabular output produced for Promoter 2.0

7:9b45a8743100

def make_tabular(raw_handle, out_handle):
    """Parse text output into tabular, return query count."""
    identifier = None
    queries = 0
    #out.write("#Identifier\tDescription\tPosition\tScore\tLikelihood\n")
    for line in raw_handle:
        #print repr(line)
        if not line.strip() or line == "Promoter prediction:\n":
            pass
        elif line[0] != " ":

                                  "Marginal prediction",
                                  "Medium likely prediction",
                                  "Highly likely prediction"]:
                stop_err("ERROR: Problem with line: %r" % line)
            out_handle.write("%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood))
    #out.close()
    return queries
    
working_dir, bin = get_path_and_binary()

if not os.path.isfile(fasta_file):

del results
del jobs

out_handle = open(tabular_file, "w")
out_handle.write("#Identifier\tDescription\tPosition\tScore\tLikelihood\n")
queries = 0
for temp in temp_files:
    data_handle = open(temp)
    count = make_tabular(data_handle, out_handle)
    data_handle.close()

8:976a5f2833cd

def make_tabular(raw_handle, out_handle):
    """Parse text output into tabular, return query count."""
    identifier = None
    queries = 0
    for line in raw_handle:
        #print repr(line)
        if not line.strip() or line == "Promoter prediction:\n":
            pass
        elif line[0] != " ":

                                  "Marginal prediction",
                                  "Medium likely prediction",
                                  "Highly likely prediction"]:
                stop_err("ERROR: Problem with line: %r" % line)
            out_handle.write("%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood))
    return queries
    
working_dir, bin = get_path_and_binary()

if not os.path.isfile(fasta_file):

del results
del jobs

out_handle = open(tabular_file, "w")
out_handle.write("#Identifier\tPosition\tScore\tLikelihood\n")
queries = 0
for temp in temp_files:
    data_handle = open(temp)
    count = make_tabular(data_handle, out_handle)
    data_handle.close()