Beispiel #1
0
def parse_roi():
    bed = cftr.parse_bedfile(cftr.RESOURCE['amplicon_bed'])
    regions = []
    for chrom in bed.keys():
        for start in sorted(bed[chrom].keys()):
            name = bed[chrom][start]['NAME']
            regions.append([chrom, start, bed[chrom][start]['END'], name])
    sys.stderr.write("ROI: {} regions\n".format(len(regions)))
    return regions
Beispiel #2
0
def parse_roi(state=False):
    bedfile = cftr.RESOURCE['analysis_roi_bed'] if state else \
              cftr.RESOURCE['covered_roi_bed']
    bed = cftr.parse_bedfile(bedfile)
    regions = []
    for chrom in bed.keys():
        for start in sorted(bed[chrom].keys()):
            name = bed[chrom][start]['NAME']
            regions.append([chrom, start, bed[chrom][start]['END'], name])
    sys.stderr.write("ROI: {} regions\n".format(len(regions)))
    return regions
Beispiel #3
0
def parse_roi(state=False):
    bedfile = cftr.RESOURCE['analysis_roi_bed'] if state else \
              cftr.RESOURCE['covered_roi_bed']
    bed = cftr.parse_bedfile(bedfile)
    regions = []
    for chrom in bed.keys():
        for start in sorted(bed[chrom].keys()):
            name = bed[chrom][start]['NAME']
            regions.append([chrom, start, bed[chrom][start]['END'], name])
    sys.stderr.write("ROI: {} regions\n".format(len(regions)))
    return regions
                        " .variant_function and" +\
                        " .exonic_variant_function files.", )
    parser.add_argument("-o", "--outdir", help="Directory for output file.",)
    parser.add_argument("-l", "--label", help="Label for output file.",)
    parser.add_argument("-f", "--force", default=False, action='store_true',
                        help="Overwrite existing files.")

    if len(sys.argv)<2:
        parser.print_help()
        sys.exit()
    args = parser.parse_args()

    outlabel = get_outlabel(args.vcffiles, args)
    outfile = outlabel + ".results.txt"
    rejectfile = outlabel + ".rejects.txt"
    if have_file(outfile, args.force):
        sys.stderr.write("  Already have {}.\n".format(outfile))
    else:
        flatdata = defaultdict(dict)
        for vcffile in args.vcffiles:
            (fields, vcfdata) = parse_vcf(vcffile)
            (flatdata, newfields) = flatten_vcf_data(fields, vcfdata, flatdata)
        annovar_data = get_annovar_data(args.annovar)
        bedfile = cftr.RESOURCE['analysis_roi_bed']
        if not os.path.isfile(bedfile): 
            sys.exit("BED file {} not found\n".format(bedfile))
        roi = cftr.parse_bedfile(bedfile)
        create_spreadsheet(newfields, flatdata, annovar_data, roi, outfile,
                           rejectfile, args)

Beispiel #5
0
                        help="Minimum QD to report (default 2.0).",)
    parser.add_argument("--maxfs", type=float, default=30.0,
                        help="Maximum FS to report (default 30.0).",)
    parser.add_argument("-f", "--force", default=False, action='store_true',
                        help="Overwrite existing files.")

    if len(sys.argv)<2:
        parser.print_help()
        sys.exit()
    args = parser.parse_args()

    outlabel = get_outlabel(args.vcffiles, args)
    outfile = outlabel + ".results.txt"
    rejectfile = outlabel + ".rejects.txt"
    if have_file(outfile, args.force):
        sys.stderr.write("  Already have {}.\n".format(outfile))
    else:
        flatdata = defaultdict(dict)
        for vcffile in args.vcffiles:
            (fields, vcfdata) = parse_vcf(vcffile)
            (flatdata, newfields) = flatten_vcf_data(fields, vcfdata, flatdata)
        add_depth_info(args.depths, flatdata, newfields, args)
        annovar_data = get_annovar_data(args.annovar)
        bedfile = cftr.RESOURCE['analysis_roi_bed']
        if not os.path.isfile(bedfile): 
            sys.exit("BED file {} not found\n".format(bedfile))
        roi = cftr.parse_bedfile(bedfile)
        create_spreadsheet(newfields, flatdata, annovar_data, roi, outfile,
                           rejectfile, args)