"*.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(
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",
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",
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,
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,
"*.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(
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
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,
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",
"-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(
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(
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",
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,
