def main():
## this function performs dispatch on the command line that a user proves. Look at the first argument, which specifies he functio nthe user wants rPGA to perform, then dispatch to the appropriate module.
parser = argparse.ArgumentParser(description='rPGA')
parser.add_argument('command',nargs='*') ## command user wants to run
## multiple modules
parser.add_argument('--gz',help='flag denoting gzipped reads',action='store_true') ## gzipped reads (for mapping) or VCF file (for everything else)
parser.add_argument('-e',help="file containing RNA editing positions, downloaded from RADAR") #for
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('-v',help="VCF genotype directory") ## or vcf file if just providing one
parser.add_argument('-g',help="GTF annotation file")
parser.add_argument('-o',help="output directory")
parser.add_argument('--nmask',help="flag to N-mask reference genome and align to that",action="store_true")
## personalize parameters
parser.add_argument('-r',help="reference fasta file")
## mapping parameters
parser.add_argument('-N',help="number of mismatches per read pair")
parser.add_argument('-T',help="num threads for STAR alignment")
parser.add_argument('-M',help="max number of multiple alignments in STAR mapping")
parser.add_argument('-s',help="fastq read file(s), comma deliminated if paired end")
parser.add_argument('-r1',help="hap1 reference genome file")#personal genome, if providing own
parser.add_argument('-r2',help="hap2 reference genome file") # personal genome, if providing own
parser.add_argument('-rn',help="N-masked reference genome file") # if providing own
parser.add_argument('--readlength',help="read length, used to generate genome index (see STAR parameter sjdbOverhang)")
parser.add_argument('--genomedir',help="STAR genome index directory (if user is providing own genome index to use for mapping)")
parser.add_argument('--hap',help="only map reads to hap1 and hap2 personal genomes",action="store_true")
## discover/assign parameters
parser.add_argument('-c',help='chromsome') #if not provided, assume run all chromsosomes
parser.add_argument('--conflict',help='flag to print conflicting reads',action='store_true')
parser.add_argument('-b1',help="haplotype 1 bam file") ## alignments to personal genomes, if providing own
parser.add_argument('-b2',help="haplotype 2 bam file")## alignments to personal genomes, if providing own
parser.add_argument('-br',help="reference alignment bam file")
parser.add_argument('--nomerge',help="flag to not merge chromosome bam files",action="store_true")
## splicing parameters
parser.add_argument('--hap1Bam', help="provide own hap1 allele specific bam file")
parser.add_argument('--hap2Bam', help="provide own hap2 allele specific bam file")
parser.add_argument('--asdir',help='directory containing AS events')
parser.add_argument('--MXE')
parser.add_argument('--SE')
parser.add_argument('--RI')
parser.add_argument('--A3SS')
parser.add_argument('--A5SS')
parser.add_argument('--samples',help="sample file for merging")
parser.add_argument('--merge',help="merge count files for multiple samples",action="store_true")
parser.add_argument('--pos2id',help="flag to change snp pos to snp id in count files",action="store_true")
parser.add_argument('--haplotype',help="flag to do hap1 vs hap2", action="store_true")
parser.add_argument('--anchorlength', help="anchor length used for STAR alignment (default=8)")
parser.add_argument('--mxeDetail',help="merge mxe detailed read counts",action="store_true")
# parser.add_argument('--exonreads',help="to include exon reads")
args = parser.parse_args()
command = args.command
if ((args.rnaedit and not args.e) or (args.e and not args.rnaedit)):
sys.stderr.write("rPGA2: if --rnaedit flag is used, you must also provide a file containing RNA editing locations using -e parameter \n")
sys.exit()
if len(command)==0:
sys.stderr.write('rPGA2: need a command - personalize, mapping, discover, alleles, splicing\n')
sys.exit()
if (not args.o):
sys.stderr.write("rPGA2: -o outDir parameter is required\n")
sys.exit()
elif command[0]=="personalize":
personalize.main(args)
elif command[0]=="mapping":
mapping.main(args)
elif command[0]=="discover":
discover.main(args)
elif command[0]=="assign":
assign.main(args)
elif command[0]=="splicing":
splicing.main(args)
else:
sys.stderr.write("rPGA: I don't recognise the option '" + command[0] +"'\n")
sys.exit()
def main():
## this function performs dispatch on the command line that a user proves. Look at the first argument, which specifies he functio nthe user wants pairadise2 to perform, then dispatch to the appropriate module.
parser = argparse.ArgumentParser(description='pairadise2')
parser.add_argument('command', nargs='*') ## command user wants to run
## multiple modules
parser.add_argument(
'--gz', help='flag denoting gzipped reads', action='store_true'
) ## gzipped reads (for mapping) or VCF file (for everything else)
parser.add_argument(
'-e',
help="file containing RNA editing positions, downloaded from RADAR"
) #for
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(
'-v',
help="VCF genotype directory") ## or vcf file if just providing one
parser.add_argument('-g', help="GTF annotation file")
parser.add_argument('-o', help="output directory")
parser.add_argument(
'--nmask',
help="flag to N-mask reference genome and align to that",
action="store_true")
## personalize parameters
parser.add_argument('-r', help="reference fasta file")
## mapping parameters
parser.add_argument('-N', help="number of mismatches per read pair")
parser.add_argument('-T', help="num threads for STAR alignment")
parser.add_argument(
'-M', help="max number of multiple alignments in STAR mapping")
parser.add_argument(
'-s', help="fastq read file(s), comma deliminated if paired end")
parser.add_argument(
'-r1',
help="hap1 reference genome file") #personal genome, if providing own
parser.add_argument(
'-r2',
help="hap2 reference genome file") # personal genome, if providing own
parser.add_argument(
'-rn', help="N-masked reference genome file") # if providing own
parser.add_argument(
'--readlength',
help=
"read length, used to generate genome index (see STAR parameter sjdbOverhang)"
)
parser.add_argument(
'--genomedir',
help=
"STAR genome index directory (if user is providing own genome index to use for mapping)"
)
parser.add_argument(
'--hap',
help="only map reads to hap1 and hap2 personal genomes",
action="store_true")
## discover/assign parameters
parser.add_argument(
'-c', help='chromsome') #if not provided, assume run all chromsosomes
parser.add_argument('--conflict',
help='flag to print conflicting reads',
action='store_true')
parser.add_argument('-b1', help="haplotype 1 bam file"
) ## alignments to personal genomes, if providing own
parser.add_argument('-b2', help="haplotype 2 bam file"
) ## alignments to personal genomes, if providing own
parser.add_argument('-br', help="reference alignment bam file")
parser.add_argument('--nomerge',
help="flag to not merge chromosome bam files",
action="store_true")
## splicing parameters
parser.add_argument('--hap1Bam',
help="provide own hap1 allele specific bam file")
parser.add_argument('--hap2Bam',
help="provide own hap2 allele specific bam file")
parser.add_argument('--asdir', help='directory containing AS events')
parser.add_argument('--MXE')
parser.add_argument('--SE')
parser.add_argument('--RI')
parser.add_argument('--A3SS')
parser.add_argument('--A5SS')
parser.add_argument('--samples', help="sample file for merging")
parser.add_argument('--merge',
help="merge count files for multiple samples",
action="store_true")
parser.add_argument('--pos2id',
help="flag to change snp pos to snp id in count files",
action="store_true")
parser.add_argument('--haplotype',
help="flag to do hap1 vs hap2",
action="store_true")
parser.add_argument(
'--anchorlength',
help="anchor length used for STAR alignment (default=8)")
parser.add_argument('--mxeDetail',
help="merge mxe detailed read counts",
action="store_true")
## assa parameters
parser.add_argument(
'--sampleDirList',
help=
"The file contains sample directory.Each directory path a row. Do not include the haplotype bam file."
)
parser.add_argument('--ASASOutDir',
help="The output folder of ASAS event count result.")
# parser.add_argument('--exonreads',help="to include exon reads")
args = parser.parse_args()
command = args.command
if ((args.rnaedit and not args.e) or (args.e and not args.rnaedit)):
sys.stderr.write(
"pairadise22: if --rnaedit flag is used, you must also provide a file containing RNA editing locations using -e parameter \n"
)
sys.exit()
if len(command) == 0:
sys.stderr.write(
'pairadise2: need a command - personalize, mapping, discover, alleles, splicing, assaevent, statistics\n'
)
sys.exit()
if (not args.o):
sys.stderr.write("pairadise2: -o outDir parameter is required\n")
sys.exit()
elif command[0] == "personalize":
personalize.main(args)
elif command[0] == "mapping":
mapping.main(args)
elif command[0] == "discover":
discover.main(args)
elif command[0] == "assign":
assign.main(args)
elif command[0] == "splicing":
splicing.main(args)
elif command[0] == "asasevent":
asasevent.main(args)
elif command[0] == "statistics":
statistics.main(args)
else:
sys.stderr.write("pairadise2: I don't recognise the option '" +
command[0] + "'\n")
sys.exit()
import os import sys import discover os.chdir(os.path.abspath(os.path.dirname(__file__)) + '/..') sys.path += ['../'] os.system(['clear', 'cls'][os.name == 'nt']) discover.main()