def main() :
"""
This function just performs dispatch on the command line that a user
provided. Basically, look at the first argument, which specifies the
function the user wants rPGA to perform, then dispatch to the appropriate
module.
"""
parser = argparse.ArgumentParser(description='rPGA')
parser.add_argument('command',nargs='*')
parser.add_argument('-N',help="number of mismatches per read pair")
parser.add_argument('-T',help="num threads for STAR alignment")
parser.add_argument('-c',help='chromsome')
parser.add_argument('--writeBam',help='flag to write allele specific bam files',action='store_true')
# parser.add_argument('-p',help='multiprocessing flag',action='store_true')
parser.add_argument('--gz',help='flag denoting gzipped reads',action='store_true')
parser.add_argument('--conflict',help='flag to print conflicting reads',action='store_true')
parser.add_argument('-M',help="max number of multiple alignments in STAR mapping")
parser.add_argument('-e',help="file containing RNA editing positions, downloaded from RADAR")
parser.add_argument('--rnaedit',help="flag to check for RNA editing events, must also provide an RNA editing file usng -e parameter",action="store_true")
parser.add_argument('--printall',help="flag to print all non haplotype specific reads in bam file output",action='store_true')
parser.add_argument('--consensus',help="flag to print consensus BAM file",action='store_true')
parser.add_argument('-b1',help="haplotype 1 bam file")
parser.add_argument('-b2',help="haplotype 2 bam file")
parser.add_argument('-br',help="reference alignment bam file")
parser.add_argument('-v',help="VCF genotype directory")
parser.add_argument('-g',help="GTF annotation file")
parser.add_argument('-o',help="output directory")
parser.add_argument('-s',help="fastq read file(s), comma deliminated if paired end")
parser.add_argument('-r',help="reference fasta file")
parser.add_argument('--nmask',help="flag to N-mask reference genome and align to that",action="store_true")
args = parser.parse_args()
command = args.command
if ((args.rnaedit and not args.e) or (args.e and not args.rnaedit)):
sys.stderr.write("rPGA: if --rnaedit flag is used, you must also provide a file containing RNA editing locations using -e parameter \n")
sys.exit()
if (not args.o):
sys.stderr.write("rPGA: -o outDir parameter is required\n")
sys.exit()
if len(command)==0:
sys.stderr.write("rPGA: need a command - init, genomes, genotype, junctions, sequences, or run \n'" )
print helpStr
# elif command[0]=="init":
# init.main(command[1:])
# elif command[0] == "genomes" :
# genomes.main(command[1:])
# elif command[0] == "genotype" :
# genotype.main(command[1:])
# elif command[0] == "junctions" :
# junctions.main(command[1:])
# elif command[0] == "sequences" :
# seqs.main(command[1:])
elif command[0] == "run" :
running.main(args)
elif command[0] == "merge":
merge.main(args)
else :
sys.stderr.write("rPGA: I don't recognise the option '" + command[0] +\
"'.\n")
def run(args):
for mt in testModels4:
import merge
model = mt[0]
test = mt[1]
print(test)
if len(mt) == 3:
args.sequence_size = mt[2]
args.test = test
merge.main(args, model)
def main():
# Save option
option = int(show_menu())
# Go through
if option == 1:
devmenu.main()
elif option == 2:
merge.main()
elif option == 3:
build.main()
elif option == 4:
setup.main()
elif option == 5:
quit()
def main(pChunkList):
print "ChunkList:"
for pChunk in pChunkList:
print pChunk
PrintHint("Begin Export Scene")
raw_input("press enter to work...")
lChunkInfo, lFlag = CreateFbx("terrain", pChunkList)
PrintHint("Export Scene Finish")
PrintHint("Begin Merge")
raw_input("press enter to work...")
merge.main(lChunkInfo, pChunkList[0], lFlag)
def main(options, args):
# check directories exist
for study in args:
if not os.path.exists(study):
print >> ERROR_FILE, 'Study cannot be found: ' + study
sys.exit(2)
study_id = os.path.basename(study)
# go through each study, and rename files to the names accepted by merge script
files_list = os.listdir(study)
for file in files_list:
if file in filenames_map:
os.rename(study + '/' + file,
study + '/' + filenames_map[file])
outputdir_files_to_rename[
study + '/' + filenames_map[file]] = study + '/' + file
if file.startswith('data_cna_hg19.seg') or file.startswith(
'meta_cna_hg19_seg') or file.startswith(
'data_cna_hg18.seg') or file.startswith(
'meta_cna_hg18_seg'):
os.rename(study + '/' + file,
study + '/' + study_id + '_' + file)
outputdir_files_to_rename[study + '/' + study_id + '_' +
file] = study + '/' + file
# call the main merge and subset script
merge.main(options, args)
# once the merge is complete, rename files back to their old names in input directories.
for key in outputdir_files_to_rename:
os.rename(key, outputdir_files_to_rename[key])
# update the file names in output directory to new naming patterns
output_directory = options.outputdir
output_studyid = options.studyid
for file in os.listdir(output_directory):
if file in filenames_map.values():
filename = get_key(file)
os.rename(output_directory + '/' + file,
output_directory + '/' + filename)
if 'data_cna_hg19' in file or 'meta_cna_hg19_seg' in file or 'data_cna_hg18' in file or 'meta_cna_hg18_seg' in file:
filename = file.replace(output_studyid + '_', '')
os.rename(output_directory + '/' + file,
output_directory + '/' + filename)
def main():
num = 1
m = int(raw_input("The number of demand:"))
n = int(raw_input("The number of facility:"))
hbar = int(raw_input("Quantity Limit H-bar:"))
dbar = int(raw_input("Distance Matrix D-bar:"))
fbar = int(raw_input("Fix Cost Limit F-bar:"))
# run random to generate random nums
generator.main(num, m, n, hbar, dbar, fbar)
prelamda = np.array([100] * m) #init lamda
while True:
# split the random nums and generate j subdata files
coor = split.main(
prelamda) #three element: 1. demand_coor 2, supply_coor 3. hi
# solve each submodel and save the ampl solution
submod.main(n)
# merge the sols
returnitem = merge.main(m, n) #returnitem = [Xi,Yi,Z,subgrad]
os.system("rm -f label_prop_output.txt")
if i == 1:
os.system("junto config simple_config")
else:
os.system("touch dump")
os.system("junto config simple_config > dump")
print '+--- output for part', i, 'generated'
#return to main STEP dir for next parts
os.chdir("..")
nope = (5, 10, 12, 18, 22, 24)
# i is the iterator to run all parts
print '+--- Initiate Graph Generation ---+\n'
for i in range(1, 31):
#part removed
if i in nope:
print '\npart', i, 'ignored\n'
continue
else:
#use input for graph
print '\nRunning part', i, '\n'
graph.main(i)
merge.main(i)
print 'Part', i, 'graph generated\n'
juntofy(i)
time.sleep(0.5)
def main():
usage = "Usage: vcfPytools.py [tool] [options]\n\n" + \
"Available tools:\n" + \
" annotate:\n\tAnnotate the vcf file with membership in other vcf files.\n" + \
" extract:\n\tExtract vcf records from a region.\n" + \
" filter:\n\tFilter the vcf file.\n" + \
" indel:\n\tIndel manipulation tools.\n" + \
" intersect:\n\tGenerate the intersection of two vcf files.\n" + \
" merge:\n\tMerge a list of vcf files.\n" + \
" multi:\n\tFind the intersections and unique fractions of multiple vcf files.\n" + \
" sort:\n\tSort a vcf file.\n" + \
" stats:\n\tGenerate statistics from a vcf file.\n" + \
" union:\n\tGenerate the union of two vcf files.\n" + \
" unique:\n\tGenerate the unique fraction from two vcf files.\n" + \
" validate:\n\tValidate the input vcf file.\n\n" + \
"vcfPytools.py [tool] --help for information on a specific tool."
# Determine the requested tool.
if len(sys.argv) > 1:
tool = sys.argv[1]
else:
print >> sys.stderr, usage
exit(1)
if tool == "annotate":
import annotate
success = annotate.main()
elif tool == "extract":
import extract
success = extract.main()
elif tool == "filter":
import filter
success = filter.main()
elif tool == "intersect":
import intersect
success = intersect.main()
elif tool == "indel":
import indel
success = indel.main()
elif tool == "multi":
import multi
success = multi.main()
elif tool == "merge":
import merge
success = merge.main()
elif tool == "sort":
import sort
success = sort.main()
elif tool == "stats":
import stats
success = stats.main()
elif tool == "union":
import union
success = union.main()
elif tool == "unique":
import unique
success = unique.main()
elif tool == "test":
import test
success = test.main()
elif tool == "validate":
import validate
success = validate.main()
elif tool == "--help" or tool == "-h" or tool == "?":
print >> sys.stderr, usage
else:
print >> sys.stderr, "Unknown tool: ", tool
print >> sys.stderr, "\n", usage
exit(1)
# If program completed properly, terminate.
if success == 0: exit(0)
'--sequence_size',
type=int,
help='size of the lstm sequence only works for LSTM and Merge',
default=5)
args = parser.parse_args()
if args.FFNN == True:
if args.run_test == True:
import FFNNtest
FFNNtest.run(args)
else:
import FFNN
FFNN.main(args)
elif args.LSTM == True:
if args.run_test == True:
import LSTMtest
LSTMtest.run(args)
else:
import LSTM
LSTM.main(args)
elif args.MERGE == True:
if args.run_test == True:
import mergetest
mergetest.run(args)
else:
import merge
merge.main(args)
else:
print("Must select a type")
def merge_worker():
import merge
merge.main()
def main():
usage = "Usage: vcfPytools.py [tool] [options]\n\n" + \
"Available tools:\n" + \
" annotate:\n\tAnnotate the vcf file with membership in other vcf files.\n" + \
" extract:\n\tExtract vcf records from a region.\n" + \
" filter:\n\tFilter the vcf file.\n" + \
" indel:\n\tIndel manipulation tools.\n" + \
" intersect:\n\tGenerate the intersection of two vcf files.\n" + \
" merge:\n\tMerge a list of vcf files.\n" + \
" multi:\n\tFind the intersections and unique fractions of multiple vcf files.\n" + \
" sort:\n\tSort a vcf file.\n" + \
" stats:\n\tGenerate statistics from a vcf file.\n" + \
" union:\n\tGenerate the union of two vcf files.\n" + \
" unique:\n\tGenerate the unique fraction from two vcf files.\n" + \
" validate:\n\tValidate the input vcf file.\n\n" + \
"vcfPytools.py [tool] --help for information on a specific tool."
# Determine the requested tool.
if len(sys.argv) > 1:
tool = sys.argv[1]
else:
print >> sys.stderr, usage
exit(1)
if tool == "annotate":
import annotate
success = annotate.main()
elif tool == "extract":
import extract
success = extract.main()
elif tool == "filter":
import filter
success = filter.main()
elif tool == "intersect":
import intersect
success = intersect.main()
elif tool == "indel":
import indel
success = indel.main()
elif tool == "multi":
import multi
success = multi.main()
elif tool == "merge":
import merge
success = merge.main()
elif tool == "sort":
import sort
success = sort.main()
elif tool == "stats":
import stats
success = stats.main()
elif tool == "union":
import union
success = union.main()
elif tool == "unique":
import unique
success = unique.main()
elif tool == "test":
import test
success = test.main()
elif tool == "validate":
import validate
success = validate.main()
elif tool == "--help" or tool == "-h" or tool == "?":
print >> sys.stderr, usage
else:
print >> sys.stderr, "Unknown tool: ",tool
print >> sys.stderr, "\n", usage
exit(1)
# If program completed properly, terminate.
if success == 0: exit(0)
