def main(command_line_args=None):
"""
:param command_line_args:
"""
VersionDependencies.python_check()
if not command_line_args:
command_line_args = sys.argv
parser = argparse.ArgumentParser(
description="A package to process Synthetic Lethal Data.\n {0} v{1}".
format(__package__, __version__),
formatter_class=RawTextHelpFormatter)
parser.add_argument('--options_file',
action='store',
dest='options_file',
required=True,
help='File containing program parameters.')
# Convert universal variables intended as boolean from string to boolean.
args, options_parser = string_to_boolean(Tool_Box.options_file(parser))
# Check file names and paths for errors
error_checking(args)
log = Tool_Box.Logger(args)
Tool_Box.log_environment_info(log, args, command_line_args)
start_time = time.time()
module_name = "Synthetic_Lethal"
log.info(
"{0} v{1}; Module: Synthetic Lethal Analysis v{2} Beginning".format(
__package__, __version__, Synthetic_Lethal.__version__))
synthetic_lethal = Synthetic_Lethal.SyntheticLethal(log, args)
if args.TargetSearch:
synthetic_lethal.fastq_analysis()
elif args.Statistics:
synthetic_lethal.statistics()
else:
log.error('No module selected to run.')
warning = "\033[1;31m **See warnings above**\033[m" if log.warning_occurred else ''
elapsed_time = int(time.time() - start_time)
log.info(
"****Völundr {0} complete ({1} seconds, {2} Mb peak memory).****\n{3}".
format(module_name, elapsed_time, Tool_Box.peak_memory(), warning))
def string_to_boolean(parser):
"""
Converts strings to boolean. Done to keep the eval() function out of the code.
:param parser:
:return:
"""
options_parser = Tool_Box.options_file(parser)
args = options_parser.parse_args()
options_parser.set_defaults(PairedEnd=bool(strtobool(args.PairedEnd)))
options_parser.set_defaults(Build_PhiX_DataFrame=bool(strtobool(args.Build_PhiX_DataFrame)))
args = options_parser.parse_args()
return args, options_parser
def main(command_line_args=None):
VersionDependencies.python_check()
if not command_line_args:
command_line_args = sys.argv
run_start = datetime.datetime.today().strftime("%a %b %d %H:%M:%S %Y")
parser = argparse.ArgumentParser(description="A little ditty to manipulate FASTQ files.\n {0} v{1}"
.format(__package__, __version__), formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('--options_file', action='store', dest='options_file', required=True,
help='File containing program parameters.')
options_parser = Tool_Box.options_file(parser)
args = options_parser.parse_args()
# args, options_parser = string_to_boolean(args, options_parser)
options_parser.set_defaults(Trim5=0)
options_parser.set_defaults(Trim3=0)
options_parser.set_defaults(Minimum_Length=100)
options_parser.set_defaults(N_Limit=100)
options_parser.set_defaults(HaloPLEX=False)
options_parser.set_defaults(ThruPLEX=False)
options_parser.set_defaults(FASTQ_PreProcess=True)
args = options_parser.parse_args()
# Check options file for errors.
error_checking(args)
log = Tool_Box.Logger(args)
Tool_Box.log_environment_info(log, args, command_line_args)
start_time = time.time()
module_name = ""
# Initialize generator to read each FASTQ file
fastq1 = FASTQ_Tools.FASTQ_Reader(args.FASTQ1, log)
fastq2 = FASTQ_Tools.FASTQ_Reader(args.FASTQ2, log)
index1 = FASTQ_Tools.FASTQ_Reader(args.Index1, log)
index2 = FASTQ_Tools.FASTQ_Reader(args.Index2, log)
splitter_data = FASTQ_Tools.FastqSplitter(args, log, fastq1, fastq2, index1, index2, paired_end=True)
new_fastq1, new_fastq2 = splitter_data.file_writer()
warning = "\033[1;31m **See warnings above**\033[m" if log.warning_occurred else ''
elapsed_time = int(time.time() - start_time)
log.info("****FASTQ Preprocessing {0} complete ({1} seconds, {2} Mb peak memory).****"
.format(module_name, elapsed_time, Tool_Box.peak_memory(), warning))
def string_to_boolean(parser):
"""
Converts strings to boolean. Done to keep the eval() function out of the code.
:param parser:
:return:
"""
options_parser = Tool_Box.options_file(parser)
args = options_parser.parse_args()
if args.IndelProcessing == "True":
# Tool_Box.debug_messenger("Pear set to FALSE.")
options_parser.set_defaults(PEAR=True)
options_parser.set_defaults(
Demultiplex=bool(strtobool(args.Demultiplex)))
options_parser.set_defaults(
OutputRawData=bool(strtobool(args.OutputRawData)))
options_parser.set_defaults(
DeleteConsensusFASTQ=bool(strtobool(args.DeleteConsensusFASTQ)))
options_parser.set_defaults(
IndelProcessing=bool(strtobool(args.IndelProcessing)))
options_parser.set_defaults(Verbose=args.Verbose.upper())
return options_parser.parse_args()
def main(command_line_args=None):
"""
:param command_line_args:
"""
VersionDependencies.python_check()
if not command_line_args:
command_line_args = sys.argv
parser = argparse.ArgumentParser(
description="A package to process Synthetic Lethal Data.\n {0} v{1}".
format(__package__, __version__),
formatter_class=RawTextHelpFormatter)
parser.add_argument('--options_file',
action='store',
dest='options_file',
required=True,
help='File containing program parameters.')
options_parser = Tool_Box.options_file(parser)
args = options_parser.parse_args()
# If we are doing statistical analysis the user will not input an Index_Mismatch value
if not getattr(args, "Index_Mismatch", False):
options_parser.add_argument("--Index_Mismatch",
dest="Index_Mismatch",
default=0)
options_parser.add_argument("--Analyze_Unknowns",
dest="Analyze_Unknowns",
default="False")
args = options_parser.parse_args()
log = Tool_Box.Logger(args)
Tool_Box.log_environment_info(log, args, command_line_args)
start_time = time.time()
module_name = "Synthetic_Lethal"
log.info(
"{0} v{1}; Module: Synthetic Lethal Analysis v{2} Beginning".format(
__package__, __version__, Synthetic_Lethal.__version__))
# Convert universal variables intended as boolean from string to boolean.
# ToDo: Should be a cleaner method to do this.
if args.Target_Search == "True":
options_parser.set_defaults(Target_Search=True)
if args.RevComp == "True":
options_parser.set_defaults(RevComp=True)
else:
options_parser.set_defaults(RevComp=False)
if args.Delete_Demultiplexed_FASTQ == "True":
options_parser.set_defaults(Delete_Demultiplexed_FASTQ=True)
else:
options_parser.set_defaults(Delete_Demultiplexed_FASTQ=False)
if args.compress == "True":
options_parser.set_defaults(compress=True)
else:
options_parser.set_defaults(compress=False)
else:
options_parser.set_defaults(Target_Search=False)
if args.Statistics == "True":
options_parser.set_defaults(Statistics=True)
else:
options_parser.set_defaults(Statistics=False)
if args.Analyze_Unknowns == "True":
options_parser.set_defaults(Analyze_Unknowns=True)
else:
options_parser.set_defaults(Analyze_Unknowns=False)
args = options_parser.parse_args()
synthetic_lethal = Synthetic_Lethal.SyntheticLethal(log, args)
# Add some parameters to our options parser object.
args = options_parser.parse_args()
if args.Target_Search:
synthetic_lethal.fastq_analysis()
elif args.Statistics:
synthetic_lethal.statistics()
else:
log.error('No module selected to run.')
warning = "\033[1;31m **See warnings above**\033[m" if log.warning_occurred else ''
elapsed_time = int(time.time() - start_time)
log.info(
"****Volundr {0} complete ({1} seconds, {2} Mb peak memory).****\n{3}".
format(module_name, elapsed_time, Tool_Box.peak_memory(), warning))
def string_conversions(parser):
"""
Convert True/False statements in parameter file to boolean
:param parser:
:return:
"""
options_parser = Tool_Box.options_file(parser)
initial_args = options_parser.parse_args()
options_parser.set_defaults(
TargetSearch=bool(strtobool(initial_args.TargetSearch)))
options_parser.set_defaults(
Statistics=bool(strtobool(initial_args.Statistics)))
options_parser.set_defaults(Verbose=initial_args.Verbose.upper())
if initial_args.Statistics == "False":
options_parser.set_defaults(
AnchorSeq=initial_args.AnchorSeq.upper())
options_parser.set_defaults(Analyze_Unknowns=bool(
strtobool(initial_args.Analyze_Unknowns)))
options_parser.set_defaults(Delete_Demultiplexed_FASTQ=bool(
strtobool(initial_args.Delete_Demultiplexed_FASTQ)))
options_parser.set_defaults(
RevComp=bool(strtobool(initial_args.RevComp)))
options_parser.set_defaults(BatchSize=int(initial_args.BatchSize))
options_parser.set_defaults(
Target_Mismatch=int(initial_args.Target_Mismatch))
options_parser.set_defaults(
MinimumReadLength=int(initial_args.MinimumReadLength))
options_parser.set_defaults(N_Limit=10)
options_parser.set_defaults(
Target_Length=int(initial_args.Target_Length))
options_parser.set_defaults(
Target_Start=int(initial_args.Target_Start))
# options_parser.set_defaults(Index_Mismatch=int(initial_args.Index_Mismatch))
options_parser.set_defaults(Spawn=int(initial_args.Spawn))
options_parser.set_defaults(
Target_Padding=int(initial_args.Target_Padding))
options_parser.set_defaults(
Expected_Position=int(initial_args.Expected_Position))
options_parser.set_defaults(
AnchorMismatch=int(initial_args.AnchorMismatch))
options_parser.set_defaults(
AnchorStart=int(initial_args.AnchorStart))
options_parser.set_defaults(
AnchorStop=int(initial_args.AnchorStop))
else:
options_parser.set_defaults(
Write_TDnorm_Log2_sgRNA_Control_File=bool(
strtobool(
initial_args.Write_TDnorm_Log2_sgRNA_Control_File)))
options_parser.set_defaults(
Write_TDnorm_Log2_sgRNA_Sample_File=bool(
strtobool(
initial_args.Write_TDnorm_Log2_sgRNA_Sample_File)))
options_parser.set_defaults(Write_Log2_sgRNA_File=bool(
strtobool(initial_args.Write_Log2_sgRNA_File)))
options_parser.set_defaults(Write_Permuted_Log2_Data_File=bool(
strtobool(initial_args.Write_Permuted_Log2_Data_File)))
options_parser.set_defaults(Bad_sgRNA_Lower_Percentile=float(
initial_args.Bad_sgRNA_Lower_Percentile))
options_parser.set_defaults(Bad_sgRNA_Upper_Percentile=float(
initial_args.Bad_sgRNA_Upper_Percentile))
options_parser.set_defaults(
UpperPercentile=float(initial_args.UpperPercentile))
options_parser.set_defaults(
LowerPercentile=float(initial_args.LowerPercentile))
options_parser.set_defaults(
PermutationCount=int(initial_args.PermutationCount))
options_parser.set_defaults(Alpha=float(initial_args.Alpha))
options_parser.set_defaults(
Target_Mismatch=float(initial_args.Target_Mismatch))
options_parser.set_defaults(
UpperGuideLimit=float(initial_args.UpperGuideLimit))
options_parser.set_defaults(
LowerGuideLimit=float(initial_args.LowerGuideLimit))
initial_args = options_parser.parse_args()
return initial_args
plot_data_dict[data_pair[6]][5].append(data_pair[4])
plot_data_dict[data_pair[6]][6].append(data_pair[5])
plot_data_dict[data_pair[6]][7].append(color_dict[data_pair[6]])
count = len(plot_data_dict[data_pair[6]][0])
if count > 1:
previous = plot_data_dict[data_pair[6]][0][count - 2]
plot_data_dict[data_pair[6]][8]\
.append(plot_data_dict[data_pair[6]][8][count - 2] + 0.0007 + (0.5*previous) + data_pair[0] * 0.5)
return plot_data_dict
# This is here to run the module as a stand-alone.
if __name__ == '__main__':
ToolBox.debug_messenger("Standing Alone")
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('--options_file',
action='store',
dest='options_file',
required=True,
help='File containing program parameters.')
options_parser = ToolBox.options_file(parser)
args = options_parser.parse_args()
scarmapperplot(args)