Python OptionGroup.add_option 예제들

예제 #1

파일: readCounts.py 프로젝트: grahnavard/NGS

                              "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r",
                  "--readalignments",
                  type="files",
                  dest="alignments",
                  default=None,
                  help="Read alignment files in indexed BAM format. Required.",
                  name="Read Alignment Files",
                  notNone=True,
                  remember=True,
                  filetypes=[("Read Alignment Files (indexed BAM)", "*.bam")])
advanced.add_option(
    "-m",
    "--minreads",
    type="int",
    dest="minreads",
    default=10,
    remember=True,
    help=
    "Minimum number of good reads at SNV locus per alignment file. Default=10.",
    name="Min. Reads")
advanced.add_option(
    "-M",
    "--maxreads",
    type="float",
    dest="maxreads",
    default=None,
    remember=True,
    help=
    "Scale read counts at high-coverage loci to ensure at most this many good reads at SNV locus per alignment file. Values greater than 1 indicate absolute read counts, otherwise the value indicates the coverage distribution percentile. Default=No maximum.",
    name="Max. Reads")
advanced.add_option(

예제 #2

파일: snv_computation.py 프로젝트: qingnanl/NGS

parser.add_option("--cosmic",
                  type="file",
                  dest="cosmic",
                  default=None,
                  help="COSMIC Mutants.",
                  filetypes=[("COSMIC Annotations", "*.tsv;*.tsv.gz")])
parser.add_option("--darned",
                  type="file",
                  dest="darned",
                  default=None,
                  help="DARNED annotations.",
                  filetypes=[("DARNED Annotations", "*.txt")])
regexs.add_option(
    "--normaldnare",
    type="str",
    dest="normaldnare",
    default=r'GDNA',
    help="Germline/Normal DNA filename regular expression. Default: GDNA.",
    remember=True,
    name="Germline DNA RE")
regexs.add_option(
    "--normaltransre",
    type="str",
    dest="normaltransre",
    default=r'NRNA',
    help="Normal transcriptome filename regular expression. Default: NRNA.",
    remember=True,
    name="Normal Transcr. RE")
regexs.add_option(
    "--tumordnare",
    type="str",
    dest="tumordnare",

예제 #3

parser.add_option("-r",
                  "--readalignments",
                  type="files",
                  dest="alignments",
                  default=None,
                  help="Read alignments in BAM/SAM format. Required.",
                  name="Read Alignments",
                  notNone=True,
                  remember=True,
                  filetypes=[("Read Alignments (BAM/SAM Format)",
                              "*.bam;*.sam")])
advanced.add_option(
    "-M",
    "--mincount",
    type="int",
    dest="mincount",
    default=3,
    remember=True,
    help=
    "Minimum number of reads for reference and variant allelels to apply LoH test. Default: 3.",
    name="Min. Count")
advanced.add_option(
    "-F",
    "--full",
    action="store_true",
    dest="full",
    default=False,
    remember=True,
    help="Output extra diagnostic read count fields. Default=False.",
    name="All Fields")
advanced.add_option("-U",
                    "--uniquereads",

예제 #4

파일: readCounts.py 프로젝트: HorvathLab/NGS

    error_kwargs = {'exit': False}
    sys.excepthook = excepthook
else:
    parser = OptionParser(version=VERSION)
    error_kwargs = {}

advanced = OptionGroup(parser, "Advanced")
parser.add_option("-s", "--snvs", type="files", dest="snvs", default=None,
                  help="Single-Nucleotide-Variant files. Required.", name="SNV Files",
                  notNone=True, remember=True,
                  filetypes=[("SNV Files", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r", "--readalignments", type="files", dest="alignments", default=None,
                  help="Read alignment files in indexed BAM format. Required.", name="Read Alignment Files",
                  notNone=True, remember=True,
                  filetypes=[("Read Alignment Files (indexed BAM)", "*.bam")])
advanced.add_option("-m", "--minreads", type="int", dest="minreads", default=10, remember=True,
                    help="Minimum number of good reads at SNV locus per alignment file. Default=10.", name="Min. Reads")
advanced.add_option("-M", "--maxreads", type="float", dest="maxreads", default=None, remember=True,
                    help="Scale read counts at high-coverage loci to ensure at most this many good reads at SNV locus per alignment file. Values greater than 1 indicate absolute read counts, otherwise the value indicates the coverage distribution percentile. Default=No maximum.", name="Max. Reads")
advanced.add_option("-F", "--full", action="store_true", dest="full", default=False, remember=True,
                    help="Output extra diagnostic read count fields. Default=False.", name="All Fields")
advanced.add_option("-f", "--alignmentfilter", action="store_false", dest="filter", default=True, remember=True,
                    help="(Turn off) alignment filtering by length, edits, etc.", name="Filter Alignments")
advanced.add_option("-U", "--uniquereads", action="store_true", dest="unique", default=False, remember=True,
                    help="Consider only distinct reads.", name="Unique Reads")
advanced.add_option("-t", "--threadsperbam", type="int", dest="tpb", default=0, remember=True,
                    help="Worker threads per alignment file. Indicate no threading with 0. Default=0.", name="Threads/BAM")
advanced.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True,
                    help="Quiet.", name="Quiet")
advanced.add_option("-d", "--debug", action="store_true", dest="debug", default=False, remember=True,
                    help="Debug.", name="Debug")
parser.add_option("-o", "--output", type="savefile", dest="output", remember=True,

예제 #5

파일: SNPlice.py 프로젝트: HorvathLab/NGS

advanced = OptionGroup(parser, "Advanced")
parser.add_option("-s", "--snps", type="files", dest="snps", default=None,
                  help="Single-Nucleotide-Polymophisms. Required.", name="SNPs",
                  notNone=True, remember=True,
                  filetypes=[("SNPs", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-j", "--junctions", type="files", dest="junctions", default=None,
                  help="Splice junctions. Required.", name="Splice Junctions",
                  notNone=True, remember=True,
                  filetypes=[("Splice Junctions (BED Format)", "*.bed")])
parser.add_option("-r", "--readalignments", type="files", dest="alignments", default=None,
                  help="Read alignments in BAM/SAM format. Required.", name="Read Alignments",
                  notNone=True, remember=True,
                  filetypes=[("Read Alignments (BAM/SAM Format)", "*.bam;*.sam")])
advanced.add_option("-d", "--distance", type="int", dest="dist", default=50, remember=True,
                    help="Upper bound on the distance between SNP locus and splice junction. Default: 50.",
                    name="Distance Bound")
advanced.add_option("-R", "--readthrough", type="int", dest="readthrough", default=5, remember=True,
                    help="Number of bases aligning into intron. Default: 5bp.",
                    name="Read-Through")
advanced.add_option("-M", "--matepairs", action="store_true", dest="mates", default=False, remember=True,
                    help="Consider the mate-pair reads for the detection of splicing. Default=False.", name="Mates")
advanced.add_option("-F", "--full", action="store_true", dest="full", default=False, remember=True,
                    help="Output extra diagnostic read count fields. Default=False.", name="All Fields")
advanced.add_option("-f", "--alignmentfilter", action="store_false", dest="filter", default=True, remember=True,
                    help="(Turn off) alignment filtering by length, edits, etc.", name="Filter Alignments")
advanced.add_option("-U", "--uniquereads", action="store_true", dest="unique", default=False, remember=True,
                    help="Consider only distinct reads.", name="Unique Reads")
advanced.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True,
                    help="Quiet.", name="Quiet")
parser.add_option("-o", "--output", type="savefile", dest="output", remember=True,

예제 #6

파일: phasedReadCounts.py 프로젝트: nalomran/NGS

                              "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r",
                  "--readalignments",
                  type="files",
                  dest="alignments",
                  default=None,
                  help="Read alignment files in indexed BAM format. Required.",
                  name="Read Alignment Files",
                  notNone=True,
                  remember=True,
                  filetypes=[("Read Alignment Files (indexed BAM)", "*.bam")])
advanced.add_option(
    "-m",
    "--minreads",
    type="int",
    dest="minreads",
    default=10,
    remember=True,
    help=
    "Minimum number of good reads at SNV locus per alignment file. Default=10.",
    name="Min. Reads")
advanced.add_option(
    "-M",
    "--minphased",
    type="int",
    dest="minphased",
    default=10,
    remember=True,
    help=
    "Minimum number of phased reads at SNV locus summed over all alignment files. Default=10.",
    name="Min. Phased")
advanced.add_option(

예제 #7

파일: snv_computation.py 프로젝트: HorvathLab/NGS

from optparse_gui import OptionParser, OptionGroup, ProgressText
parser = OptionParser(version=VERSION)
regexs = OptionGroup(parser, "Filename Matching")

parser.add_option("--counts", type="file", dest="counts", default=None,
                  help="Output file from readCounts. Required.", notNone=True,
                  filetypes=[("readCount Output", "*.tsv")])
parser.add_option("--cosmic", type="file", dest="cosmic", default=None,
                  help="COSMIC Mutants.",
                  filetypes=[("COSMIC Annotations", "*.tsv;*.tsv.gz")])
parser.add_option("--darned", type="file", dest="darned", default=None,
                  help="DARNED annotations.",
                  filetypes=[("DARNED Annotations", "*.txt")])
regexs.add_option("--normaldnare", type="str", dest="normaldnare", default=r'GDNA',
                  help="Germline/Normal DNA filename regular expression. Default: GDNA.",
                  remember=True, name="Germline DNA RE")
regexs.add_option("--normaltransre", type="str", dest="normaltransre", default=r'NRNA',
                  help="Normal transcriptome filename regular expression. Default: NRNA.",
                  remember=True, name="Normal Transcr. RE")
regexs.add_option("--tumordnare", type="str", dest="tumordnare", default=r'SDNA',
                  help="Somatic/Tumor DNA filename regular expression. Default: SDNA.",
                  remember=True, name="Somatic DNA RE")
regexs.add_option("--tumortransre", type="str", dest="tumortransre", default=r'TRNA',
                  help="Tumor transcriptome filename regular expression. Default: TRNA.",
                  remember=True, name="Tumor Transcr. RE")
parser.add_option_group(regexs)                 

opt, args = parser.parse_args()
regex = {}
regex["GDNA"] = opt.normaldnare

예제 #8

파일: RNA2DNAlign.py 프로젝트: HorvathLab/NGS

    error_kwargs = {}
						
exfilt = OptionGroup(parser, "Filtering")
readcounts = OptionGroup(parser, "Read Counting")
regexs = OptionGroup(parser, "Filename Matching")
snvannot = OptionGroup(parser, "SNV Annotation")
parser.add_option("-s", "--snvs", type="files", dest="snvs", default=None,
                  help="Single-Nucleotide-Variant files. Required.", name="SNV Files",
                  notNone=True, remember=True,
                  filetypes=[("SNV Files", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r", "--readalignments", type="files", dest="alignments", default=None,
                  help="Read alignment files in indexed BAM format. Required.", name="Read Alignment Files",
                  notNone=True, remember=True,
                  filetypes=[("Read Alignment Files (Indexed BAM)", "*.bam")])
exfilt.add_option("-e", "--exoncoords", type="file", dest="exoncoords", default=None,
                  help="Exon coordinates for SNV filtering. Optional.", name="Exon Coords.",
                  remember=True,
                  filetypes=[("Exonic Coordinates", "*.txt")])
regexs.add_option("--normaldnare", type="str", dest="normaldnare", default='GDNA',
                  help="Germline/Normal DNA filename regular expression. Default: GDNA.",
                  remember=True, name="Germline DNA")
regexs.add_option("--normaltransre", type="str", dest="normaltransre", default='NRNA',
                  help="Normal transcriptome filename regular expression. Default: NRNA.",
                  remember=True, name="Normal Transcr.")
regexs.add_option("--tumordnare", type="str", dest="tumordnare", default='SDNA',
                  help="Somatic/Tumor DNA filename regular expression. Default: SDNA.",
                  remember=True, name="Somatic DNA")
regexs.add_option("--tumortransre", type="str", dest="tumortransre", default='TRNA',
                  help="Tumor transcriptome filename regular expression. Default: TRNA.",
                  remember=True, name="Tumor Transcr.")
snvannot.add_option("-d", "--darned", type="file", dest="darned", default="",
                    help="DARNED Annotations. Optional.", remember=True,

예제 #9

파일: SNPlice.py 프로젝트: qingnanl/NGS

parser.add_option("-r",
                  "--readalignments",
                  type="files",
                  dest="alignments",
                  default=None,
                  help="Read alignments in BAM/SAM format. Required.",
                  name="Read Alignments",
                  notNone=True,
                  remember=True,
                  filetypes=[("Read Alignments (BAM/SAM Format)",
                              "*.bam;*.sam")])
advanced.add_option("-e",
                    "--exoncoords",
                    type="file",
                    dest="exoncoords",
                    default=None,
                    help="Exon coordinates for SNV filtering. Optional.",
                    name="Exon Coords.",
                    remember=True,
                    filetypes=[("Exonic Coordinates", "*.txt")])
advanced.add_option(
    "-d",
    "--distance",
    type="int",
    dest="dist",
    default=50,
    remember=True,
    help=
    "Upper bound on the distance between SNP locus and splice junction. Default: 50.",
    name="Distance Bound")
advanced.add_option("-R",

예제 #10

파일: LoH.py 프로젝트: HorvathLab/NGS

    "-r",
    "--readalignments",
    type="files",
    dest="alignments",
    default=None,
    help="Read alignments in BAM/SAM format. Required.",
    name="Read Alignments",
    notNone=True,
    remember=True,
    filetypes=[("Read Alignments (BAM/SAM Format)", "*.bam;*.sam")],
)
advanced.add_option(
    "-M",
    "--mincount",
    type="int",
    dest="mincount",
    default=3,
    remember=True,
    help="Minimum number of reads for reference and variant allelels to apply LoH test. Default: 3.",
    name="Min. Count",
)
advanced.add_option(
    "-F",
    "--full",
    action="store_true",
    dest="full",
    default=False,
    remember=True,
    help="Output extra diagnostic read count fields. Default=False.",
    name="All Fields",
)
advanced.add_option(

예제 #11

                  remember=True,
                  filetypes=[("Read Alignment Files (indexed BAM)", "*.bam")])
parser.add_option("-f",
                  "--alignmentfilter",
                  type="choice",
                  dest="filter",
                  default=filter_default,
                  remember=True,
                  help="Alignment filtering strategy. Default: Basic.",
                  choices=filterOptions,
                  name="Alignment Filter")
advanced.add_option(
    "-m",
    "--minreads",
    type="int",
    dest="minreads",
    default=minreads_default,
    remember=True,
    help=
    "Minimum number of good reads at SNV locus per alignment file. Default=5.",
    name="Min. Reads")
advanced.add_option(
    "-M",
    "--maxreads",
    type="string",
    dest="maxreads",
    default=maxreads_default,
    remember=True,
    help=
    "Scale read counts at high-coverage loci to ensure at most this many good reads at SNV locus per alignment file. Values greater than 1 indicate absolute read counts, otherwise the value indicates the coverage distribution percentile. Default=No maximum.",
    name="Max. Reads")
advanced.add_option(

예제 #12

파일: SNPlice.py 프로젝트: kk7nc/NGS

parser.add_option("-r",
                  "--readalignments",
                  type="files",
                  dest="alignments",
                  default=None,
                  help="Read alignments in BAM/SAM format. Required.",
                  name="Read Alignments",
                  notNone=True,
                  remember=True,
                  filetypes=[("Read Alignments (BAM/SAM Format)",
                              "*.bam;*.sam")])
advanced.add_option(
    "-d",
    "--distance",
    type="int",
    dest="dist",
    default=50,
    remember=True,
    help=
    "Upper bound on the distance between SNP locus and splice junction. Default: 50.",
    name="Distance Bound")
advanced.add_option("-R",
                    "--readthrough",
                    type="int",
                    dest="readthrough",
                    default=5,
                    remember=True,
                    help="Number of bases aligning into intron. Default: 5bp.",
                    name="Read-Through")
advanced.add_option(
    "-M",
    "--matepairs",

예제 #13

파일: RNA2DNAlign.py 프로젝트: qingnanl/NGS

    error_kwargs = {}
                                                
exfilt = OptionGroup(parser, "Filtering")
readcounts = OptionGroup(parser, "Read Counting")
regexs = OptionGroup(parser, "Filename Matching")
snvannot = OptionGroup(parser, "SNV Annotation")
parser.add_option("-s", "--snvs", type="files", dest="snvs", default=None,
                  help="Single-Nucleotide-Variant files. Required.", name="SNV Files",
                  notNone=True, remember=True,
                  filetypes=[("SNV Files", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r", "--readalignments", type="files", dest="alignments", default=None,
                  help="Read alignment files in indexed BAM format. Required.", name="Read Alignment Files",
                  notNone=True, remember=True,
                  filetypes=[("Read Alignment Files (Indexed BAM)", "*.bam")])
exfilt.add_option("-e", "--exoncoords", type="file", dest="exoncoords", default=None,
                  help="Exon coordinates for SNV filtering. Optional.", name="Exon Coords.",
                  remember=True,
                  filetypes=[("Exonic Coordinates", "*.txt")])
regexs.add_option("--normaldnare", type="str", dest="normaldnare", default='GDNA',
                  help="Germline/Normal DNA filename regular expression. Default: GDNA.",
                  remember=True, name="Germline DNA")
regexs.add_option("--normaltransre", type="str", dest="normaltransre", default='NRNA',
                  help="Normal transcriptome filename regular expression. Default: NRNA.",
                  remember=True, name="Normal Transcr.")
regexs.add_option("--tumordnare", type="str", dest="tumordnare", default='SDNA',
                  help="Somatic/Tumor DNA filename regular expression. Default: SDNA.",
                  remember=True, name="Somatic DNA")
regexs.add_option("--tumortransre", type="str", dest="tumortransre", default='TRNA',
                  help="Tumor transcriptome filename regular expression. Default: TRNA.",
                  remember=True, name="Tumor Transcr.")
snvannot.add_option("-d", "--darned", type="file", dest="darned", default="",
                    help="DARNED Annotations. Optional.", remember=True,