def _prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = """usage: %prog <-g genome_fasta> <-1 first fastq file> [ -2 second fastq file -n sample_name]"""
description = """This script will align read in Sanger fastq format to a reference genome and create a bam file. using bwa and samtools"""
prog_version=utils.getWtss_version()
optparser = OptionParser(version="%prog of wtss_pipeline v"+prog_version,description=description,usage=usage,add_help_option=False)
optparser.add_option("-h","--help",action="help",help="show this help message and exit.")
optparser.add_option("-g","--genome_file",dest="genome_file",type="string",
help="Path to a fasta file where the genome is located. Default: %default")
optparser.add_option("-1","--fastq1",dest="fastq_file1",type="string",
help="Path to the first fastq file where the first reads are. This file is mandatory. Default: %default")
optparser.add_option("-2","--fastq2",dest="fastq_file2",type="string",
help="Path to the second fastq file where the second reads are. This file is optional. Default: %default")
optparser.add_option("-o","--output_dir",dest="output_dir",type="string",
help="The path to the directory where the results will be output. If not set, the results will be put in the same folder as fastq1. Default: %default")
optparser.add_option("-n","--name",dest="name",type="string",
help="The name of the sample currently being aligned. Default: %default")
optparser.add_option("-t", "--thread",dest="thread",type='int',default=1,
help="Number of thread used by the alignment algorithm. Default: %default")
optparser.add_option("--illumina",dest="illumina",action='store_true',default=False,
help="the fastq file are in illumina 1.3-1.6 fastq format. Default: %default")
optparser.add_option("--print",dest="print_commands",action='store_true',default=False,
help="Print the command instead of running them. Default: %default")
optparser.add_option("--fifo",dest="fifo",action='store_true',default=False,
help="Use fifo to avoid writing big temp file to the disk. Default: %default")
optparser.add_option("-r", "--readgroup",dest="read_group",type="string",help="Set read group for SAM file:\n"+"Example: RG\tID:uid\tSM:sample\tPL:Illumina\n")
return optparser
def _prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = """usage: %prog -b <bam_file>"""
description = """This script will remove duplicate from a bam file based on the first read reference and the second read sequence."""
prog_version=utils.getWtss_version()
optparser = OptionParser(version="%prog of wtss_pipeline v"+prog_version,description=description,usage=usage,add_help_option=False)
optparser.add_option("-h","--help",action="help",help="show this help message and exit.")
optparser.add_option("-b","--input_bam",dest="input_bam",type="string",
help="Path to input bam file. Default: %default")
return optparser
def _prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = """usage: %prog -b <bam_file>"""
description = """This script will remove duplicate from a bam file based on the first read reference and the second read sequence."""
prog_version = utils.getWtss_version()
optparser = OptionParser(version="%prog of wtss_pipeline v" + prog_version,
description=description,
usage=usage,
add_help_option=False)
optparser.add_option("-h",
"--help",
action="help",
help="show this help message and exit.")
optparser.add_option("-b",
"--input_bam",
dest="input_bam",
type="string",
help="Path to input bam file. Default: %default")
return optparser
def _prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = """usage: %prog <-g genome_fasta> <-1 first fastq file> [ -2 second fastq file -n sample_name]"""
description = """This script will align read in Sanger fastq format to a reference genome and create a bam file. using bwa and samtools"""
prog_version=utils.getWtss_version()
optparser = OptionParser(version="%prog of wtss_pipeline v"+prog_version,description=description,usage=usage,add_help_option=False)
optparser.add_option("-h","--help",action="help",help="show this help message and exit.")
optparser.add_option("-g","--genome_file",dest="genome_file",type="string",
help="Path to a fasta file where the genome is located. Default: %default")
optparser.add_option("-1","--fastq1",dest="fastq_file1",type="string",
help="Path to the first fastq file where the first reads are. This file is mandatory. Default: %default")
optparser.add_option("-2","--fastq2",dest="fastq_file2",type="string",
help="Path to the second fastq file where the second reads are. This file is optional. Default: %default")
optparser.add_option("-o","--output_dir",dest="output_dir",type="string",
help="The path to the directory where the results will be output. If not set, the results will be put in the same folder as fastq1. Default: %default")
optparser.add_option("-n","--name",dest="name",type="string",
help="The name of the sample currently being aligned. Default: %default")
optparser.add_option("-s", "--sort",dest="sort",action='store_true',default=False,
help="Sort the bam file by coordinates at the end of the alignment. Default: %default")
optparser.add_option("-t", "--thread",dest="thread",type='int',default=1,
help="Number of thread used by the alignment algorithm. Default: %default")
optparser.add_option("--illumina",dest="illumina",action='store_true',default=False,
help="the fastq file are in illumina 1.3-1.6 fastq format. Default: %default")
optparser.add_option("--print",dest="print_commands",action='store_true',default=False,
help="Print the command instead of running them. Default: %default")
help_rna_seq="%s --> increase the maximum insert size to 20kb.\n"%(ANALYSIS_RNA_SEQ)
help_digit_transc="%s --> prevent any gap in the tag.\n"%(ANALYSIS_DIGITAL_TRANSC)
optparser.add_option("--analysis",dest="analysis",type="string",default=None,
help="Set analysis specific parameters:\n"+help_rna_seq+help_digit_transc+"Default: %default")
optparser.add_option("-r", "--readgroup",dest="read_group",type="string",help="Set read group for SAM file:\n"+"Example: RG\tID:uid\tSM:sample\tPL:Illumina\n")
return optparser
def _prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = """usage: %prog <-g genome_fasta> <-1 first fastq file> [ -2 second fastq file -n sample_name]"""
description = """This script will align read in Sanger fastq format to a reference genome and create a bam file. using bwa and samtools"""
prog_version = utils.getWtss_version()
optparser = OptionParser(version="%prog of wtss_pipeline v" + prog_version,
description=description,
usage=usage,
add_help_option=False)
optparser.add_option("-h",
"--help",
action="help",
help="show this help message and exit.")
optparser.add_option(
"-g",
"--genome_file",
dest="genome_file",
type="string",
help=
"Path to a fasta file where the genome is located. Default: %default")
optparser.add_option(
"-1",
"--fastq1",
dest="fastq_file1",
type="string",
help=
"Path to the first fastq file where the first reads are. This file is mandatory. Default: %default"
)
optparser.add_option(
"-2",
"--fastq2",
dest="fastq_file2",
type="string",
help=
"Path to the second fastq file where the second reads are. This file is optional. Default: %default"
)
optparser.add_option(
"-o",
"--output_dir",
dest="output_dir",
type="string",
help=
"The path to the directory where the results will be output. If not set, the results will be put in the same folder as fastq1. Default: %default"
)
optparser.add_option(
"-n",
"--name",
dest="name",
type="string",
help="The name of the sample currently being aligned. Default: %default"
)
optparser.add_option(
"-s",
"--sort",
dest="sort",
action='store_true',
default=False,
help=
"Sort the bam file by coordinates at the end of the alignment. Default: %default"
)
optparser.add_option(
"-t",
"--thread",
dest="thread",
type='int',
default=1,
help=
"Number of thread used by the alignment algorithm. Default: %default")
optparser.add_option(
"--illumina",
dest="illumina",
action='store_true',
default=False,
help=
"the fastq file are in illumina 1.3-1.6 fastq format. Default: %default"
)
optparser.add_option(
"--print",
dest="print_commands",
action='store_true',
default=False,
help="Print the command instead of running them. Default: %default")
help_rna_seq = "%s --> increase the maximum insert size to 20kb.\n" % (
ANALYSIS_RNA_SEQ)
help_digit_transc = "%s --> prevent any gap in the tag.\n" % (
ANALYSIS_DIGITAL_TRANSC)
optparser.add_option("--analysis",
dest="analysis",
type="string",
default=None,
help="Set analysis specific parameters:\n" +
help_rna_seq + help_digit_transc +
"Default: %default")
optparser.add_option("-r",
"--readgroup",
dest="read_group",
type="string",
help="Set read group for SAM file:\n" +
"Example: RG\tID:uid\tSM:sample\tPL:Illumina\n")
return optparser
def _prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = """usage: %prog <-g genome_fasta> <-1 first fastq file> [ -2 second fastq file -n sample_name]"""
description = """This script will align read in Sanger fastq format to a reference genome and create a bam file. using bwa and samtools"""
prog_version = utils.getWtss_version()
optparser = OptionParser(version="%prog of wtss_pipeline v" + prog_version,
description=description,
usage=usage,
add_help_option=False)
optparser.add_option("-h",
"--help",
action="help",
help="show this help message and exit.")
optparser.add_option(
"-g",
"--genome_file",
dest="genome_file",
type="string",
help=
"Path to a fasta file where the genome is located. Default: %default")
optparser.add_option(
"-1",
"--fastq1",
dest="fastq_file1",
type="string",
help=
"Path to the first fastq file where the first reads are. This file is mandatory. Default: %default"
)
optparser.add_option(
"-2",
"--fastq2",
dest="fastq_file2",
type="string",
help=
"Path to the second fastq file where the second reads are. This file is optional. Default: %default"
)
optparser.add_option(
"-o",
"--output_dir",
dest="output_dir",
type="string",
help=
"The path to the directory where the results will be output. If not set, the results will be put in the same folder as fastq1. Default: %default"
)
optparser.add_option(
"-n",
"--name",
dest="name",
type="string",
help="The name of the sample currently being aligned. Default: %default"
)
optparser.add_option(
"-t",
"--thread",
dest="thread",
type='int',
default=1,
help=
"Number of thread used by the alignment algorithm. Default: %default")
optparser.add_option(
"--illumina",
dest="illumina",
action='store_true',
default=False,
help=
"the fastq file are in illumina 1.3-1.6 fastq format. Default: %default"
)
optparser.add_option(
"--print",
dest="print_commands",
action='store_true',
default=False,
help="Print the command instead of running them. Default: %default")
optparser.add_option(
"--fifo",
dest="fifo",
action='store_true',
default=False,
help=
"Use fifo to avoid writing big temp file to the disk. Default: %default"
)
optparser.add_option("-r",
"--readgroup",
dest="read_group",
type="string",
help="Set read group for SAM file:\n" +
"Example: RG\tID:uid\tSM:sample\tPL:Illumina\n")
return optparser
