--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/modules/utils.py	Wed Jan 22 08:41:44 2020 -0500
@@ -0,0 +1,337 @@
+import pickle
+import traceback
+import shlex
+import subprocess
+from threading import Timer
+import shutil
+import time
+import functools
+import os.path
+import sys
+import argparse
+
+
+def start_logger(workdir):
+    time_str = time.strftime("%Y%m%d-%H%M%S")
+    sys.stdout = Logger(workdir, time_str)
+    logfile = sys.stdout.getLogFile()
+    return logfile, time_str
+
+
+class Logger(object):
+    def __init__(self, out_directory, time_str):
+        self.logfile = os.path.join(out_directory, str('run.' + time_str + '.log'))
+        self.terminal = sys.stdout
+        self.log = open(self.logfile, "w")
+
+    def write(self, message):
+        self.terminal.write(message)
+        self.log.write(message)
+        self.log.flush()
+
+    def flush(self):
+        pass
+
+    def getLogFile(self):
+        return self.logfile
+
+
+def checkPrograms(programs_version_dictionary):
+    print '\n' + 'Checking dependencies...'
+    programs = programs_version_dictionary
+    which_program = ['which', '']
+    listMissings = []
+    for program in programs:
+        which_program[1] = program
+        run_successfully, stdout, stderr = runCommandPopenCommunicate(which_program, False, None, False)
+        if not run_successfully:
+            listMissings.append(program + ' not found in PATH.')
+        else:
+            print stdout.splitlines()[0]
+            if programs[program][0] is None:
+                print program + ' (impossible to determine programme version) found at: ' + stdout.splitlines()[0]
+            else:
+                if program.endswith('.jar'):
+                    check_version = ['java', '-jar', stdout.splitlines()[0], programs[program][0]]
+                    programs[program].append(stdout.splitlines()[0])
+                else:
+                    check_version = [stdout.splitlines()[0], programs[program][0]]
+                run_successfully, stdout, stderr = runCommandPopenCommunicate(check_version, False, None, False)
+                if stdout == '':
+                    stdout = stderr
+                if program == 'wget':
+                    version_line = stdout.splitlines()[0].split(' ', 3)[2]
+                else:
+                    version_line = stdout.splitlines()[0].split(' ')[-1]
+                replace_characters = ['"', 'v', 'V', '+']
+                for i in replace_characters:
+                    version_line = version_line.replace(i, '')
+                print program + ' (' + version_line + ') found'
+                if programs[program][1] == '>=':
+                    program_found_version = version_line.split('.')
+                    program_version_required = programs[program][2].split('.')
+                    if len(program_version_required) == 3:
+                        if len(program_found_version) == 2:
+                            program_found_version.append(0)
+                        else:
+                            program_found_version[2] = program_found_version[2].split('_')[0]                           
+                    for i in range(0, len(program_version_required)):
+                        if isinstance(program_found_version[i], (int, long)):
+                            if int(program_found_version[i]) < int(program_version_required[i]):
+                                listMissings.append('It is required ' + program + ' with version ' + programs[program][1] + ' ' + programs[program][2])
+                else:
+                    if version_line != programs[program][2]:
+                        listMissings.append('It is required ' + program + ' with version ' + programs[program][1] + ' ' + programs[program][2])
+    return listMissings
+
+
+def requiredPrograms():
+    programs_version_dictionary = {}
+    programs_version_dictionary['rematch.py'] = ['--version', '>=', '3.2']
+    missingPrograms = checkPrograms(programs_version_dictionary)
+    if len(missingPrograms) > 0:
+        sys.exit('\n' + 'Errors:' + '\n' + '\n'.join(missingPrograms))
+
+
+def general_information(logfile, version, outdir, time_str):
+    # Check if output directory exists
+
+    print '\n' + '==========> patho_typing <=========='
+    print '\n' + 'Program start: ' + time.ctime()
+
+    # Tells where the logfile will be stored
+    print '\n' + 'LOGFILE:'
+    print logfile
+
+    # Print command
+    print '\n' + 'COMMAND:'
+    script_path = os.path.abspath(sys.argv[0])
+    print sys.executable + ' ' + script_path + ' ' + ' '.join(sys.argv[1:])
+
+    # Print directory where programme was lunch
+    print '\n' + 'PRESENT DIRECTORY:'
+    present_directory = os.path.abspath(os.getcwd())
+    print present_directory
+
+    # Print program version
+    print '\n' + 'VERSION:'
+    scriptVersionGit(version, present_directory, script_path)
+
+    # Check programms
+    requiredPrograms()
+
+    return script_path
+
+
+def setPATHvariable(doNotUseProvidedSoftware, script_path):
+    path_variable = os.environ['PATH']
+    script_folder = os.path.dirname(script_path)
+    # Set path to use provided softwares
+    if not doNotUseProvidedSoftware:
+        bowtie2 = os.path.join(script_folder, 'src', 'bowtie2-2.2.9')
+        samtools = os.path.join(script_folder, 'src', 'samtools-1.3.1', 'bin')
+        bcftools = os.path.join(script_folder, 'src', 'bcftools-1.3.1', 'bin')
+
+        os.environ['PATH'] = str(':'.join([bowtie2, samtools, bcftools, path_variable]))
+
+    # Print PATH variable
+    print '\n' + 'PATH variable:'
+    print os.environ['PATH']
+
+
+def scriptVersionGit(version, directory, script_path):
+    print 'Version ' + version
+
+    try:
+        os.chdir(os.path.dirname(script_path))
+        command = ['git', 'log', '-1', '--date=local', '--pretty=format:"%h (%H) - Commit by %cn, %cd) : %s"']
+        run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
+        print stdout
+        command = ['git', 'remote', 'show', 'origin']
+        run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
+        print stdout
+        os.chdir(directory)
+    except:
+        print 'HARMLESS WARNING: git command possibly not found. The GitHub repository information will not be obtained.'
+
+
+def runTime(start_time):
+    end_time = time.time()
+    time_taken = end_time - start_time
+    hours, rest = divmod(time_taken, 3600)
+    minutes, seconds = divmod(rest, 60)
+    print 'Runtime :' + str(hours) + 'h:' + str(minutes) + 'm:' + str(round(seconds, 2)) + 's'
+    return round(time_taken, 2)
+
+
+def timer(function, name):
+    @functools.wraps(function)
+    def wrapper(*args, **kwargs):
+        print('\n' + 'RUNNING {0}\n'.format(name))
+        start_time = time.time()
+
+        results = list(function(*args, **kwargs))  # guarantees return is a list to allow .insert()
+
+        time_taken = runTime(start_time)
+        print('END {0}'.format(name))
+
+        results.insert(0, time_taken)
+        return results
+    return wrapper
+
+
+def removeDirectory(directory):
+    if os.path.isdir(directory):
+        shutil.rmtree(directory)
+
+
+def saveVariableToPickle(variableToStore, pickleFile):
+    with open(pickleFile, 'wb') as writer:
+        pickle.dump(variableToStore, writer)
+
+
+def extractVariableFromPickle(pickleFile):
+    with open(pickleFile, 'rb') as reader:
+        variable = pickle.load(reader)
+    return variable
+
+
+def trace_unhandled_exceptions(func):
+    @functools.wraps(func)
+    def wrapped_func(*args, **kwargs):
+        try:
+            func(*args, **kwargs)
+        except:
+            print 'Exception in ' + func.__name__
+            traceback.print_exc()
+    return wrapped_func
+
+
+def kill_subprocess_Popen(subprocess_Popen, command):
+    print 'Command run out of time: ' + str(command)
+    subprocess_Popen.kill()
+
+
+def runCommandPopenCommunicate(command, shell_True, timeout_sec_None, print_comand_True):
+    run_successfully = False
+    if not isinstance(command, basestring):
+        command = ' '.join(command)
+    command = shlex.split(command)
+
+    if print_comand_True:
+        print 'Running: ' + ' '.join(command)
+
+    if shell_True:
+        command = ' '.join(command)
+        proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
+    else:
+        proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+    not_killed_by_timer = True
+    if timeout_sec_None is None:
+        stdout, stderr = proc.communicate()
+    else:
+        timer = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
+        timer.start()
+        stdout, stderr = proc.communicate()
+        timer.cancel()
+        not_killed_by_timer = timer.isAlive()
+
+    if proc.returncode == 0:
+        run_successfully = True
+    else:
+        if not print_comand_True and not_killed_by_timer:
+            print 'Running: ' + str(command)
+        if len(stdout) > 0:
+            print 'STDOUT'
+            print stdout.decode("utf-8")
+        if len(stderr) > 0:
+            print 'STDERR'
+            print stderr.decode("utf-8")
+    return run_successfully, stdout, stderr
+
+
+def required_length(tuple_length_options, argument_name):
+    class RequiredLength(argparse.Action):
+        def __call__(self, parser, args, values, option_string=None):
+            if len(values) not in tuple_length_options:
+                msg = 'Option {argument_name} requires one of the following number of arguments: {tuple_length_options}'.format(
+                    argument_name=self.argument_name, tuple_length_options=tuple_length_options)
+                raise argparse.ArgumentTypeError(msg)
+            setattr(args, self.dest, values)
+    return RequiredLength
+
+
+def get_sequence_information(fasta_file, length_extra_seq):
+    sequence_dict = {}
+    headers = {}
+
+    with open(fasta_file, 'rtU') as reader:
+        blank_line_found = False
+        sequence_counter = 0
+        temp_sequence_dict = {}
+        for line in reader:
+            line = line.splitlines()[0]
+            if len(line) > 0:
+                if not blank_line_found:
+                    if line.startswith('>'):
+                        if len(temp_sequence_dict) > 0:
+                            if temp_sequence_dict.values()[0]['length'] - 2 * length_extra_seq > 0:
+                                sequence_dict[temp_sequence_dict.keys()[0]] = temp_sequence_dict.values()[0]
+                                headers[temp_sequence_dict.values()[0]['header'].lower()] = sequence_counter
+                            else:
+                                print temp_sequence_dict.values()[0]['header'] + ' sequence ignored due to length <= 0'
+                            temp_sequence_dict = {}
+
+                        if line[1:].lower() in headers:
+                            sys.exit('Found duplicated sequence headers')
+
+                        sequence_counter += 1
+                        temp_sequence_dict[sequence_counter] = {'header': line[1:].lower(), 'sequence': '', 'length': 0}
+                    else:
+                        temp_sequence_dict[sequence_counter]['sequence'] += line.upper()
+                        temp_sequence_dict[sequence_counter]['length'] += len(line)
+                else:
+                    sys.exit('It was found a blank line between the fasta file above line ' + line)
+            else:
+                blank_line_found = True
+
+        if len(temp_sequence_dict) > 0:
+            if temp_sequence_dict.values()[0]['length'] - 2 * length_extra_seq > 0:
+                sequence_dict[temp_sequence_dict.keys()[0]] = temp_sequence_dict.values()[0]
+                headers[temp_sequence_dict.values()[0]['header'].lower()] = sequence_counter
+            else:
+                print temp_sequence_dict.values()[0]['header'] + ' sequence ignored due to length <= 0'
+
+    return sequence_dict, headers
+
+
+def simplify_sequence_dict(sequence_dict):
+    simple_sequence_dict = {}
+    for counter, info in sequence_dict.items():
+        simple_sequence_dict[info['header']] = info
+        del simple_sequence_dict[info['header']]['header']
+    return simple_sequence_dict
+
+
+def chunkstring(string, length):
+    return (string[0 + i:length + i] for i in range(0, len(string), length))
+
+
+def clean_headers_sequences(sequence_dict):
+    problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
+    # print 'Checking if reference sequences contain ' + str(problematic_characters) + '\n'
+
+    headers_changed = False
+    new_headers = {}
+    for i in sequence_dict:
+        if any(x in sequence_dict[i]['header'] for x in problematic_characters):
+            for x in problematic_characters:
+                sequence_dict[i]['header'] = sequence_dict[i]['header'].replace(x, '_')
+            headers_changed = True
+        new_headers[sequence_dict[i]['header'].lower()] = i
+
+    if headers_changed:
+        print 'At least one of the those characters was found. Replacing those with _' + '\n'
+
+    return sequence_dict, new_headers