test_eurl_vtec_wgs_pt: scripts/ReMatCh/modules/utils.py comparison

comparison scripts/ReMatCh/modules/utils.py @ 3:0cbed1c0a762 draft default tip

planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8

author	cstrittmatter
date	Tue, 28 Jan 2020 10:42:31 -0500
parents	965517909457
children

comparison

equal deleted inserted replaced

-:6837f733b4aa
+:0cbed1c0a762
 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
 def start_logger(workdir):
 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)
 with open(os.path.join(outdir, 'cpu_information.' + time_str + '.slurm.txt'), 'wt') as writer:
 for environment in sorted(os.environ):
 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('\n' + 'PATH variable:')
-print os.environ['PATH']
+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('.')
 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 int(program_found_version[i]) < int(program_version_required[i]):
+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])
+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:
+if SRA or SRAopt:
-programs_version_dictionary['gzip'] = ['--version', '>=', '1.6']
+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' + '==========> ReMatCh <==========')
-print '\n' + 'Program start: ' + time.ctime()
+print('\n' + 'Program start: ' + time.ctime())
 # Tells where the logfile will be stored
-print '\n' + 'LOGFILE:'
+print('\n' + 'LOGFILE:')
-print logfile
+print(logfile)
 # Print command
-print '\n' + 'COMMAND:'
+print('\n' + 'COMMAND:')
-script_path = os.path.abspath(sys.argv[0])
+script_path = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), 'rematch.py')
-print sys.executable + ' ' + script_path + ' ' + ' '.join(sys.argv[1:])
+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:'
+print('\n' + 'VERSION:')
-scriptVersionGit(version, present_directory, script_path)
+script_version_git(version, present_directory, script_path)
 # Get CPU information
 get_cpu_information(outdir, time_str)
 # Set and print PATH variable
 setPATHvariable(doNotUseProvidedSoftware, script_path)
 # Check programms
-requiredPrograms(asperaKey, downloadCramBam)
+requiredPrograms(asperaKey, downloadCramBam, SRA, SRAopt)
 return script_path
-def scriptVersionGit(version, directory, script_path):
+def script_version_git(version, current_directory, script_path, no_git_info=False):
-print 'Version ' + version
+"""
+Print script version and get GitHub commit information
-try:
-os.chdir(os.path.dirname(script_path))
+Parameters
-command = ['git', 'log', '-1', '--date=local', '--pretty=format:"%h (%H) - Commit by %cn, %cd) : %s"']
+----------
-run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
+version : str
-print stdout
+Version of the script, e.g. "4.0"
-command = ['git', 'remote', 'show', 'origin']
+current_directory : str
-run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
+Path to the directory where the script was start to run
-print stdout
+script_path : str
-os.chdir(directory)
+Path to the script running
-except:
+no_git_info : bool, default False
-print 'HARMLESS WARNING: git command possibly not found. The GitHub repository information will not be obtained.'
+True if it is not necessary to retreive the GitHub commit information
+Returns
-def runTime(start_time):
+-------
+"""
+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 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)
 return results
 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:
+except Exception as e:
-print 'Exception in ' + func.__name__
+print('Exception in ' + func.__name__)
-traceback.print_exc()
+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)
 proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
 else:
 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,))
+time_counter = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
-timer.start()
+time_counter.start()
 stdout, stderr = proc.communicate()
-timer.cancel()
+time_counter.cancel()
-not_killed_by_timer = timer.isAlive()
+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')
-print stdout.decode("utf-8")
+print(stdout.decode("utf-8"))
 if len(stderr) > 0:
-print 'STDERR'
+print('STDERR')
-print stderr.decode("utf-8")
+print(stderr.decode("utf-8"))
-return run_successfully, stdout, stderr
+return run_successfully, stdout.decode("utf-8"), stderr.decode("utf-8")
 def rchop(string, ending):
 if string.endswith(ending):
 string = string[:-len(ending)]
 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

Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

comparison scripts/ReMatCh/modules/utils.py @ 3:0cbed1c0a762 draft default tip