"*.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,