--- a/scripts/ReMatCh/modules/utils.py	Wed Jan 22 09:10:12 2020 -0500
+++ b/scripts/ReMatCh/modules/utils.py	Tue Jan 28 10:42:31 2020 -0500
@@ -1,11 +1,11 @@
 import pickle
-import traceback
+from traceback import format_exception as traceback_format_exception
 import shlex
 import subprocess
 from threading import Timer
 import shutil
 import time
-import functools
+from functools import wraps as functools_wraps
 import os.path
 import sys
 
@@ -38,7 +38,7 @@
 def get_cpu_information(outdir, time_str):
     with open(os.path.join(outdir, 'cpu_information.' + time_str + '.cpu.txt'), 'wt') as writer:
         command = ['cat', '/proc/cpuinfo']
-        run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, None, False)
+        run_successfully, stdout, stderr = run_command_popen_communicate(command, False, None, False)
         if run_successfully:
             writer.write(stdout)
 
@@ -60,41 +60,43 @@
         os.environ['PATH'] = str(':'.join([bowtie2, samtools, bcftools, path_variable]))
 
     # Print PATH variable
-    print '\n' + 'PATH variable:'
-    print os.environ['PATH']
+    print('\n' + 'PATH variable:')
+    print(os.environ['PATH'])
 
 
 def checkPrograms(programs_version_dictionary):
-    print '\n' + 'Checking dependencies...'
+    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)
+        run_successfully, stdout, stderr = run_command_popen_communicate(which_program, False, None, False)
         if not run_successfully:
             listMissings.append(program + ' not found in PATH.')
         else:
-            print stdout.splitlines()[0]
+            print(stdout.splitlines()[0])
             if programs[program][0] is None:
-                print program + ' (impossible to determine programme version) found at: ' + stdout.splitlines()[0]
+                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)
+                run_successfully, stdout, stderr = run_command_popen_communicate(check_version, False, None, False)
                 if stdout == '':
                     stdout = stderr
-                if program == 'wget':
+                if program in ['wget', 'awk']:
                     version_line = stdout.splitlines()[0].split(' ', 3)[2]
+                elif program in ['prefetch', 'fastq-dump']:
+                    version_line = stdout.splitlines()[1].split(' ')[-1]
                 else:
                     version_line = stdout.splitlines()[0].split(' ')[-1]
-                replace_characters = ['"', 'v', 'V', '+']
+                replace_characters = ['"', 'v', 'V', '+', ',']
                 for i in replace_characters:
                     version_line = version_line.replace(i, '')
-                print program + ' (' + version_line + ') found'
+                print(program + ' (' + version_line + ') found')
                 if programs[program][1] == '>=':
                     program_found_version = version_line.split('.')
                     program_version_required = programs[program][2].split('.')
@@ -104,52 +106,61 @@
                         else:
                             program_found_version[2] = program_found_version[2].split('_')[0]
                     for i in range(0, len(program_version_required)):
-                        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])
+                        if int(program_found_version[i]) > int(program_version_required[i]):
+                            break
+                        elif int(program_found_version[i]) == int(program_version_required[i]):
+                            continue
+                        else:
+                            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])
+                        listMissings.append('It is required ' + program + ' with version ' + programs[program][1] +
+                                            ' ' + programs[program][2])
     return listMissings
 
 
-def requiredPrograms(asperaKey, downloadCramBam):
+def requiredPrograms(asperaKey, downloadCramBam, SRA, SRAopt):
     programs_version_dictionary = {}
     programs_version_dictionary['wget'] = ['--version', '>=', '1.12']
+    programs_version_dictionary['gzip'] = ['--version', '>=', '1.6']
     programs_version_dictionary['bowtie2'] = ['--version', '>=', '2.2.9']
     programs_version_dictionary['samtools'] = ['--version', '==', '1.3.1']
     programs_version_dictionary['bcftools'] = ['--version', '==', '1.3.1']
     if asperaKey is not None:
         programs_version_dictionary['ascp'] = ['--version', '>=', '3.6.1']
-    if downloadCramBam:
-        programs_version_dictionary['gzip'] = ['--version', '>=', '1.6']
+    if SRA or SRAopt:
+        programs_version_dictionary['prefetch'] = ['--version', '>=', '2.8.2']
+        programs_version_dictionary['fastq-dump'] = ['--version', '>=', '2.8.2']
+        programs_version_dictionary['awk'] = ['--version', '>=', '3.0.4']
     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, doNotUseProvidedSoftware, asperaKey, downloadCramBam):
+def general_information(logfile, version, outdir, time_str, doNotUseProvidedSoftware, asperaKey, downloadCramBam, SRA, SRAopt):
     # Check if output directory exists
 
-    print '\n' + '==========> ReMatCh <=========='
-    print '\n' + 'Program start: ' + time.ctime()
+    print('\n' + '==========> ReMatCh <==========')
+    print('\n' + 'Program start: ' + time.ctime())
 
     # Tells where the logfile will be stored
-    print '\n' + 'LOGFILE:'
-    print logfile
+    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('\n' + 'COMMAND:')
+    script_path = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), 'rematch.py')
+    print(sys.executable + ' ' + ' '.join(sys.argv))
 
     # Print directory where programme was lunch
-    print '\n' + 'PRESENT DIRECTORY:'
+    print('\n' + 'PRESENT DIRECTORY:')
     present_directory = os.path.abspath(os.getcwd())
-    print present_directory
+    print(present_directory)
 
     # Print program version
-    print '\n' + 'VERSION:'
-    scriptVersionGit(version, present_directory, script_path)
+    print('\n' + 'VERSION:')
+    script_version_git(version, present_directory, script_path)
 
     # Get CPU information
     get_cpu_information(outdir, time_str)
@@ -158,45 +169,66 @@
     setPATHvariable(doNotUseProvidedSoftware, script_path)
 
     # Check programms
-    requiredPrograms(asperaKey, downloadCramBam)
+    requiredPrograms(asperaKey, downloadCramBam, SRA, SRAopt)
 
     return script_path
 
 
-def scriptVersionGit(version, directory, script_path):
-    print 'Version ' + version
+def script_version_git(version, current_directory, script_path, no_git_info=False):
+    """
+    Print script version and get GitHub commit information
+
+    Parameters
+    ----------
+    version : str
+        Version of the script, e.g. "4.0"
+    current_directory : str
+        Path to the directory where the script was start to run
+    script_path : str
+        Path to the script running
+    no_git_info : bool, default False
+        True if it is not necessary to retreive the GitHub commit information
+
+    Returns
+    -------
 
-    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.'
+    """
+    print('Version {}'.format(version))
+
+    if not no_git_info:
+        try:
+            os.chdir(os.path.dirname(os.path.dirname(script_path)))
+            command = ['git', 'log', '-1', '--date=local', '--pretty=format:"%h (%H) - Commit by %cn, %cd) : %s"']
+            run_successfully, stdout, stderr = run_command_popen_communicate(command, False, 15, False)
+            print(stdout)
+            command = ['git', 'remote', 'show', 'origin']
+            run_successfully, stdout, stderr = run_command_popen_communicate(command, False, 15, False)
+            print(stdout)
+        except:
+            print('HARMLESS WARNING: git command possibly not found. The GitHub repository information will not be'
+                  ' obtained.')
+        finally:
+            os.chdir(current_directory)
 
 
-def runTime(start_time):
+def run_time(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'
+    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)
+    @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)
+        time_taken = run_time(start_time)
         print('END {0}'.format(name))
 
         results.insert(0, time_taken)
@@ -204,47 +236,53 @@
     return wrapper
 
 
-def removeDirectory(directory):
+def remove_directory(directory):
     if os.path.isdir(directory):
         shutil.rmtree(directory)
 
 
-def saveVariableToPickle(variableToStore, outdir, prefix):
+def save_variable_to_pickle(variableToStore, outdir, prefix):
     pickleFile = os.path.join(outdir, str(prefix + '.pkl'))
     with open(pickleFile, 'wb') as writer:
         pickle.dump(variableToStore, writer)
 
 
-def extractVariableFromPickle(pickleFile):
+def extract_variable_from_pickle(pickleFile):
     with open(pickleFile, 'rb') as reader:
         variable = pickle.load(reader)
     return variable
 
 
 def trace_unhandled_exceptions(func):
-    @functools.wraps(func)
+    @functools_wraps(func)
     def wrapped_func(*args, **kwargs):
         try:
             func(*args, **kwargs)
-        except:
-            print 'Exception in ' + func.__name__
-            traceback.print_exc()
+        except Exception as e:
+            print('Exception in ' + func.__name__)
+            print(e)
+
+            exc_type, exc_value, exc_tb = sys.exc_info()
+            print(''.join(traceback_format_exception(exc_type, exc_value, exc_tb)))
+
+            raise exc_type(exc_value)
+
     return wrapped_func
 
 
 def kill_subprocess_Popen(subprocess_Popen, command):
-    print 'Command run out of time: ' + str(command)
+    print('Command run out of time: ' + str(command))
     subprocess_Popen.kill()
 
 
-def runCommandPopenCommunicate(command, shell_True, timeout_sec_None, print_comand_True):
+def run_command_popen_communicate(command, shell_True, timeout_sec_None, print_comand_True):
     run_successfully = False
-    if not isinstance(command, basestring):
+    if not isinstance(command, str):
         command = ' '.join(command)
     command = shlex.split(command)
 
     if print_comand_True:
-        print 'Running: ' + ' '.join(command)
+        print('Running: ' + ' '.join(command))
 
     if shell_True:
         command = ' '.join(command)
@@ -256,24 +294,24 @@
     if timeout_sec_None is None:
         stdout, stderr = proc.communicate()
     else:
-        timer = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
-        timer.start()
+        time_counter = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
+        time_counter.start()
         stdout, stderr = proc.communicate()
-        timer.cancel()
-        not_killed_by_timer = timer.isAlive()
+        time_counter.cancel()
+        not_killed_by_timer = time_counter.isAlive()
 
     if proc.returncode == 0:
         run_successfully = True
     else:
         if not print_comand_True and not_killed_by_timer:
-            print 'Running: ' + str(command)
+            print('Running: ' + str(command))
         if len(stdout) > 0:
-            print 'STDOUT'
-            print stdout.decode("utf-8")
+            print('STDOUT')
+            print(stdout.decode("utf-8"))
         if len(stderr) > 0:
-            print 'STDERR'
-            print stderr.decode("utf-8")
-    return run_successfully, stdout, stderr
+            print('STDERR')
+            print(stderr.decode("utf-8"))
+    return run_successfully, stdout.decode("utf-8"), stderr.decode("utf-8")
 
 
 def rchop(string, ending):
@@ -285,11 +323,11 @@
 def reverse_complement(seq):
     complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N'}
 
-    reverse_complement = ''
+    reverse_complement_string = ''
 
     seq = reversed(list(seq.upper()))
 
     for base in seq:
-        reverse_complement += complement[base]
+        reverse_complement_string += complement[base]
 
-    return reverse_complement
+    return reverse_complement_string