#!/usr/bin/env python

import argparse, sys
import math, time, re
from argparse import RawTextHelpFormatter

__author__ = "Colby Chiang (cc2qe@virginia.edu)"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2014-04-23 14:31 $"

# --------------------------------------
# define functions

def get_args():
    parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter, description="\
vcfToBedpe\n\
author: " + __author__ + "\n\
version: " + __version__ + "\n\
description: Convert a VCF file to a BEDPE file")
    parser.add_argument('-i', '--input', type=argparse.FileType('r'), default=None, help='VCF input (default: stdin)')
    parser.add_argument('-o', '--output', type=argparse.FileType('w'), default=sys.stdout, help='Output BEDPE to write (default: stdout)')

    # parse the arguments
    args = parser.parse_args()

    # if no input, check if part of pipe and if so, read stdin.
    if args.input == None:
        if sys.stdin.isatty():
            parser.print_help()
            exit(1)
        else:
            args.input = sys.stdin

    # send back the user input
    return args

class Vcf(object):
    def __init__(self):
        self.file_format = 'VCFv4.2'
        # self.fasta = fasta
        self.reference = ''
        self.sample_list = []
        self.info_list = []
        self.format_list = []
        self.alt_list = []
        self.add_format('GT', 1, 'String', 'Genotype')

    def add_header(self, header):
        for line in header:
            if line.split('=')[0] == '##fileformat':
                self.file_format = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##reference':
                self.reference = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##INFO':
                a = line[line.find('<')+1:line.find('>')]
                r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+')
                self.add_info(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##ALT':
                a = line[line.find('<')+1:line.find('>')]
                r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+')
                self.add_alt(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##FORMAT':
                a = line[line.find('<')+1:line.find('>')]
                r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+')
                self.add_format(*[b.split('=')[1] for b in r.findall(a)])
            elif line[0] == '#' and line[1] != '#':
                self.sample_list = line.rstrip().split('\t')[9:]
    # return the VCF header
    def get_header(self):
        header = '\n'.join(['##fileformat=' + self.file_format,
                            '##fileDate=' + time.strftime('%Y%m%d'),
                            '##reference=' + self.reference] + \
                           [i.hstring for i in self.info_list] + \
                           [a.hstring for a in self.alt_list] + \
                           [f.hstring for f in self.format_list] + \
                           ['\t'.join([
                               '#CHROM',
                               'POS',
                               'ID',
                               'REF',
                               'ALT',
                               'QUAL',
                               'FILTER',
                               'INFO',
                               'FORMAT'] + \
                                      self.sample_list
                                  )])
        return header

    def add_info(self, id, number, type, desc):
        if id not in [i.id for i in self.info_list]:
            inf = Info(id, number, type, desc)
            self.info_list.append(inf)

    def add_alt(self, id, desc):
        if id not in [a.id for a in self.alt_list]:
            alt = Alt(id, desc)
            self.alt_list.append(alt)

    def add_format(self, id, number, type, desc):
        if id not in [f.id for f in self.format_list]:
            fmt = Format(id, number, type, desc)
            self.format_list.append(fmt)

    def add_sample(self, name):
        self.sample_list.append(name)

class Info(object):
    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        # strip the double quotes around the string if present
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = '##INFO=<ID=' + self.id + ',Number=' + self.number + ',Type=' + self.type + ',Description=\"' + self.desc + '\">'

class Alt(object):
    def __init__(self, id, desc):
        self.id = str(id)
        self.desc = str(desc)
        # strip the double quotes around the string if present
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = '##ALT=<ID=' + self.id + ',Description=\"' + self.desc + '\">'

class Format(object):
    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        # strip the double quotes around the string if present
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = '##FORMAT=<ID=' + self.id + ',Number=' + self.number + ',Type=' + self.type + ',Description=\"' + self.desc + '\">'

class Variant(object):
    def __init__(self, var_list, vcf):
        self.chrom = var_list[0]
        self.pos = int(var_list[1])
        self.var_id = var_list[2]
        self.ref = var_list[3]
        self.alt = var_list[4]
        self.qual = var_list[5]
        self.filter = var_list[6]
        self.sample_list = vcf.sample_list
        self.info_list = vcf.info_list
        self.info = dict()
        self.format_list = vcf.format_list
        self.active_formats = list()
        self.gts = dict()
        # make a genotype for each sample at variant
        for i in range(len(self.sample_list)):
            s_gt = var_list[9+i].split(':')[0]
            s = self.sample_list[i]
            self.gts[s] = Genotype(self, s, s_gt)
        # import the existing fmt fields
        for i in range(len(self.sample_list)):
            s = self.sample_list[i]
            for j in zip(var_list[8].split(':'), var_list[9+i].split(':')):
                self.gts[s].set_format(j[0], j[1])

        self.info = dict()
        i_split = [a.split('=') for a in var_list[7].split(';')] # temp list of split info column
        for i in i_split:
            if len(i) == 1:
                i.append(True)
            self.info[i[0]] = i[1]

    def set_info(self, field, value):
        if field in [i.id for i in self.info_list]:
            self.info[field] = value
        else:
            sys.stderr.write('\nError: invalid INFO field, \"' + field + '\"\n')
            exit(1)

    def get_info(self, field):
        return self.info[field]

    def get_info_string(self):
        i_list = list()
        for info_field in self.info_list:
            if info_field.id in self.info:
                if info_field.type == 'Flag':
                    i_list.append(info_field.id)
                else:
                    i_list.append('%s=%s' % (info_field.id, self.info[info_field.id]))
        return ';'.join(i_list)

    def get_format_string(self):
        f_list = list()
        for f in self.format_list:
            if f.id in self.active_formats:
                f_list.append(f.id)
        return ':'.join(f_list)

    def genotype(self, sample_name):
        if sample_name in self.sample_list:
            return self.gts[sample_name]
        else:
            sys.stderr.write('\nError: invalid sample name, \"' + sample_name + '\"\n')

    def get_var_string(self):
        s =[
            self.chrom,
            self.pos,
            self.var_id,
            self.ref,
            self.alt,
            '%0.2f' % self.qual,
            self.filter,
            self.get_info_string(),
            self.get_format_string(),
            '\t'.join(self.genotype(s).get_gt_string() for s in self.sample_list)
        ]
        return '\t'.join(str(v) for v in s)

class Genotype(object):
    def __init__(self, variant, sample_name, gt):
        self.format = dict()
        self.variant = variant
        self.set_format('GT', gt)

    def set_format(self, field, value):
        if field in [i.id for i in self.variant.format_list]:
            self.format[field] = value
            if field not in self.variant.active_formats:
                self.variant.active_formats.append(field)
                # sort it to be in the same order as the format_list in header
                self.variant.active_formats.sort(key=lambda x: [f.id for f in self.variant.format_list].index(x))
        else:
            sys.stderr.write('\nError: invalid FORMAT field, \"' + field + '\"\n')
            exit(1)

    def get_format(self, field):
        return self.format[field]

    def get_gt_string(self):
        g_list = list()
        for f in self.variant.active_formats:
            if f in self.format:
                if type(self.format[f]) == float:
                    g_list.append('%0.2f' % self.format[f])
                else:
                    g_list.append(self.format[f])
            else:
                g_list.append('.')
        return ':'.join([str(s) for s in g_list])

# primary function
def vcfToBedpe(vcf_file, bedpe_out):
    vcf = Vcf()
    in_header = True
    header = []
    # dict of BND variant lines that have not yet been matched.
    # variant id is the key
    unmatched = dict()

    for line in vcf_file:
        if in_header:
            if line[0] == '#':
                header.append(line)
                if line[1] != '#':
                    sample_list = line.rstrip().split('\t')[9:]
                continue
            else:
                # print header
                bedpe_out.write('\t'.join(['#CHROM_A',
                                           'START_A',
                                           'END_A',
                                           'CHROM_B',
                                           'START_B',
                                           'END_B',
                                           'ID',
                                           'QUAL',
                                           'STRAND_A',
                                           'STRAND_B',
                                           'TYPE',
                                           'FILTER',
                                           'INFO',
                                           'FORMAT'] +
                                           sample_list
                                          ) + '\n')
                in_header = False
                vcf.add_header(header)

        v = line.rstrip().split('\t')
        var = Variant(v, vcf)

        if var.info['SVTYPE'] != 'BND':
            b1 = var.pos
            b2 = int(var.info['END'])
            name = v[2]
            score = v[5]

            strands = var.info['STRANDS']
            o1 = strands[0]
            o2 = strands[1]

            span = [int(i) for i in var.info['CIPOS'].split(',')]
            s1 = b1 + span[0] - 1
            e1 = b1 + span[1]

            span = [int(i) for i in var.info['CIEND'].split(',')]
            s2 = b2 + span[0] - 1
            e2 = b2 + span[1]

            ispan = s2 - e1
            ospan = e2 - s1

            ev_list = list()
            for ev in ['PE', 'SR']:
                if int(var.info[ev]) > 0:
                    ev_list.append(ev)
            evtype = ','.join(ev_list)

            format_list = v[8].split(':')
            sample_gt = dict()
            var_sample_list = []
            for i in range(len(sample_list)):
                s = sample_list[i]
                gt = v[9 + i]
                format_dict = dict(zip(format_list, gt.split(':')))
                format_dict['PE'] = int(format_dict['PE'])
                format_dict['SR'] = int(format_dict['SR'])
                format_dict['SU'] = int(format_dict['SU'])
                if format_dict['SU'] > 0:
                    var_sample_list.append(sample_list[i])
                sample_gt[s] = format_dict

            gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in sample_list])
            support = sum([sample_gt[s]['SU'] for s in sample_list])

            bed_l =[var.chrom,
                    s1,
                    e1,
                    var.chrom,
                    s2,
                    e2,
                    name,
                    var.qual,
                    o1,
                    o2,
                    var.info['SVTYPE'],
                    var.filter,
                    var.get_info_string(),
                    var.get_format_string()]
            bedpe_out.write('\t'.join(str(s) for s in bed_l + [var.gts[sample].get_gt_string() for sample in var.sample_list]) + '\n')

        else:
            mate_id = var.info['MATEID']
            if mate_id in unmatched:
                prim = unmatched[mate_id]
                sec = var

                b1 = prim.pos
                b2 = sec.pos
                score = v[5]

                strands = prim.info['STRANDS']
                o1 = strands[0]
                o2 = strands[1]

                span = [int(i) for i in prim.info['CIPOS'].split(',')]
                s1 = b1 + span[0] - 1
                e1 = b1 + span[1]

                span = [int(i) for i in sec.info['CIPOS'].split(',')]
                s2 = b2 + span[0] - 1
                e2 = b2 + span[1]

                ispan = s2 - e1
                ospan = e2 - s1

                ev_list = list()
                for ev in ['PE', 'SR']:
                    if int(var.info[ev]) > 0:
                        ev_list.append(ev)
                evtype = ','.join(ev_list)

                format_list = v[8].split(':')
                sample_gt = dict()
                var_sample_list = []
                for i in range(len(sample_list)):
                    s = sample_list[i]
                    gt = v[9 + i]
                    format_dict = dict(zip(format_list, gt.split(':')))
                    format_dict['PE'] = int(format_dict['PE'])
                    format_dict['SR'] = int(format_dict['SR'])
                    format_dict['SU'] = int(format_dict['SU'])
                    if format_dict['SU'] > 0:
                        var_sample_list.append(sample_list[i])
                    sample_gt[s] = format_dict

                gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in sample_list])
                support = sum([sample_gt[s]['SU'] for s in sample_list])

                bed_l = [prim.chrom,
                         s1,
                         e1,
                         sec.chrom,
                         s2,
                         e2,
                         prim.info['EVENT'],
                         prim.qual,
                         o1,
                         o2,
                         prim.info['SVTYPE'],
                         prim.filter,
                         prim.get_info_string(),
                         prim.get_format_string(),
                         '\t'.join([prim.gts[sample].get_gt_string() for sample in prim.sample_list])]
                bedpe_out.write('\t'.join([str(s) for s in bed_l]) + '\n')

                # delete the mate from the dictionary
                del unmatched[mate_id]
            else:
                # if the mate isn't already in the dict, add current variant to dictionary
                unmatched[var.var_id] = var

    if len(unmatched) > 0:
        sys.stderr.write("Warning: %s unmatched variants\n"
                         % len(unmatched))
    # close the files
    bedpe_out.close()
    vcf_file.close()

    return

# --------------------------------------
# wrapper function

def main():
    # parse the command line args
    args = get_args()

    # call primary function
    vcfToBedpe(args.input, args.output)

# initialize the script
if __name__ == '__main__':
    try:
        sys.exit(main())
    except IOError as e:
        if e.errno != 32:  # ignore SIGPIPE
            raise

5c49f44636d153992a6f99aea24f1c9fa30567b3
<mask token>


class Alt(object):

    def __init__(self, id, desc):
        self.id = str(id)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##ALT=<ID=' + self.id + ',Description="' + self.
            desc + '">')


class Format(object):

    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##FORMAT=<ID=' + self.id + ',Number=' + self.
            number + ',Type=' + self.type + ',Description="' + self.desc + '">'
            )


class Variant(object):

    def __init__(self, var_list, vcf):
        self.chrom = var_list[0]
        self.pos = int(var_list[1])
        self.var_id = var_list[2]
        self.ref = var_list[3]
        self.alt = var_list[4]
        self.qual = var_list[5]
        self.filter = var_list[6]
        self.sample_list = vcf.sample_list
        self.info_list = vcf.info_list
        self.info = dict()
        self.format_list = vcf.format_list
        self.active_formats = list()
        self.gts = dict()
        for i in range(len(self.sample_list)):
            s_gt = var_list[9 + i].split(':')[0]
            s = self.sample_list[i]
            self.gts[s] = Genotype(self, s, s_gt)
        for i in range(len(self.sample_list)):
            s = self.sample_list[i]
            for j in zip(var_list[8].split(':'), var_list[9 + i].split(':')):
                self.gts[s].set_format(j[0], j[1])
        self.info = dict()
        i_split = [a.split('=') for a in var_list[7].split(';')]
        for i in i_split:
            if len(i) == 1:
                i.append(True)
            self.info[i[0]] = i[1]

    def set_info(self, field, value):
        if field in [i.id for i in self.info_list]:
            self.info[field] = value
        else:
            sys.stderr.write('\nError: invalid INFO field, "' + field + '"\n')
            exit(1)

    def get_info(self, field):
        return self.info[field]

    def get_info_string(self):
        i_list = list()
        for info_field in self.info_list:
            if info_field.id in self.info:
                if info_field.type == 'Flag':
                    i_list.append(info_field.id)
                else:
                    i_list.append('%s=%s' % (info_field.id, self.info[
                        info_field.id]))
        return ';'.join(i_list)

    def get_format_string(self):
        f_list = list()
        for f in self.format_list:
            if f.id in self.active_formats:
                f_list.append(f.id)
        return ':'.join(f_list)

    def genotype(self, sample_name):
        if sample_name in self.sample_list:
            return self.gts[sample_name]
        else:
            sys.stderr.write('\nError: invalid sample name, "' +
                sample_name + '"\n')

    def get_var_string(self):
        s = [self.chrom, self.pos, self.var_id, self.ref, self.alt, '%0.2f' %
            self.qual, self.filter, self.get_info_string(), self.
            get_format_string(), '\t'.join(self.genotype(s).get_gt_string() for
            s in self.sample_list)]
        return '\t'.join(str(v) for v in s)


class Genotype(object):

    def __init__(self, variant, sample_name, gt):
        self.format = dict()
        self.variant = variant
        self.set_format('GT', gt)

    def set_format(self, field, value):
        if field in [i.id for i in self.variant.format_list]:
            self.format[field] = value
            if field not in self.variant.active_formats:
                self.variant.active_formats.append(field)
                self.variant.active_formats.sort(key=lambda x: [f.id for f in
                    self.variant.format_list].index(x))
        else:
            sys.stderr.write('\nError: invalid FORMAT field, "' + field + '"\n'
                )
            exit(1)

    def get_format(self, field):
        return self.format[field]

    def get_gt_string(self):
        g_list = list()
        for f in self.variant.active_formats:
            if f in self.format:
                if type(self.format[f]) == float:
                    g_list.append('%0.2f' % self.format[f])
                else:
                    g_list.append(self.format[f])
            else:
                g_list.append('.')
        return ':'.join([str(s) for s in g_list])


<mask token>

<mask token>


def get_args():
    parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter,
        description="""vcfToBedpe
author: """ + __author__ + '\nversion: ' +
        __version__ + """
description: Convert a VCF file to a BEDPE file""")
    parser.add_argument('-i', '--input', type=argparse.FileType('r'),
        default=None, help='VCF input (default: stdin)')
    parser.add_argument('-o', '--output', type=argparse.FileType('w'),
        default=sys.stdout, help='Output BEDPE to write (default: stdout)')
    args = parser.parse_args()
    if args.input == None:
        if sys.stdin.isatty():
            parser.print_help()
            exit(1)
        else:
            args.input = sys.stdin
    return args


class Vcf(object):

    def __init__(self):
        self.file_format = 'VCFv4.2'
        self.reference = ''
        self.sample_list = []
        self.info_list = []
        self.format_list = []
        self.alt_list = []
        self.add_format('GT', 1, 'String', 'Genotype')

    def add_header(self, header):
        for line in header:
            if line.split('=')[0] == '##fileformat':
                self.file_format = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##reference':
                self.reference = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##INFO':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_info(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##ALT':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_alt(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##FORMAT':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_format(*[b.split('=')[1] for b in r.findall(a)])
            elif line[0] == '#' and line[1] != '#':
                self.sample_list = line.rstrip().split('\t')[9:]

    def get_header(self):
        header = '\n'.join(['##fileformat=' + self.file_format, 
            '##fileDate=' + time.strftime('%Y%m%d'), '##reference=' + self.
            reference] + [i.hstring for i in self.info_list] + [a.hstring for
            a in self.alt_list] + [f.hstring for f in self.format_list] + [
            '\t'.join(['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL',
            'FILTER', 'INFO', 'FORMAT'] + self.sample_list)])
        return header

    def add_info(self, id, number, type, desc):
        if id not in [i.id for i in self.info_list]:
            inf = Info(id, number, type, desc)
            self.info_list.append(inf)

    def add_alt(self, id, desc):
        if id not in [a.id for a in self.alt_list]:
            alt = Alt(id, desc)
            self.alt_list.append(alt)

    def add_format(self, id, number, type, desc):
        if id not in [f.id for f in self.format_list]:
            fmt = Format(id, number, type, desc)
            self.format_list.append(fmt)

    def add_sample(self, name):
        self.sample_list.append(name)


class Info(object):

    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##INFO=<ID=' + self.id + ',Number=' + self.number +
            ',Type=' + self.type + ',Description="' + self.desc + '">')


class Alt(object):

    def __init__(self, id, desc):
        self.id = str(id)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##ALT=<ID=' + self.id + ',Description="' + self.
            desc + '">')


class Format(object):

    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##FORMAT=<ID=' + self.id + ',Number=' + self.
            number + ',Type=' + self.type + ',Description="' + self.desc + '">'
            )


class Variant(object):

    def __init__(self, var_list, vcf):
        self.chrom = var_list[0]
        self.pos = int(var_list[1])
        self.var_id = var_list[2]
        self.ref = var_list[3]
        self.alt = var_list[4]
        self.qual = var_list[5]
        self.filter = var_list[6]
        self.sample_list = vcf.sample_list
        self.info_list = vcf.info_list
        self.info = dict()
        self.format_list = vcf.format_list
        self.active_formats = list()
        self.gts = dict()
        for i in range(len(self.sample_list)):
            s_gt = var_list[9 + i].split(':')[0]
            s = self.sample_list[i]
            self.gts[s] = Genotype(self, s, s_gt)
        for i in range(len(self.sample_list)):
            s = self.sample_list[i]
            for j in zip(var_list[8].split(':'), var_list[9 + i].split(':')):
                self.gts[s].set_format(j[0], j[1])
        self.info = dict()
        i_split = [a.split('=') for a in var_list[7].split(';')]
        for i in i_split:
            if len(i) == 1:
                i.append(True)
            self.info[i[0]] = i[1]

    def set_info(self, field, value):
        if field in [i.id for i in self.info_list]:
            self.info[field] = value
        else:
            sys.stderr.write('\nError: invalid INFO field, "' + field + '"\n')
            exit(1)

    def get_info(self, field):
        return self.info[field]

    def get_info_string(self):
        i_list = list()
        for info_field in self.info_list:
            if info_field.id in self.info:
                if info_field.type == 'Flag':
                    i_list.append(info_field.id)
                else:
                    i_list.append('%s=%s' % (info_field.id, self.info[
                        info_field.id]))
        return ';'.join(i_list)

    def get_format_string(self):
        f_list = list()
        for f in self.format_list:
            if f.id in self.active_formats:
                f_list.append(f.id)
        return ':'.join(f_list)

    def genotype(self, sample_name):
        if sample_name in self.sample_list:
            return self.gts[sample_name]
        else:
            sys.stderr.write('\nError: invalid sample name, "' +
                sample_name + '"\n')

    def get_var_string(self):
        s = [self.chrom, self.pos, self.var_id, self.ref, self.alt, '%0.2f' %
            self.qual, self.filter, self.get_info_string(), self.
            get_format_string(), '\t'.join(self.genotype(s).get_gt_string() for
            s in self.sample_list)]
        return '\t'.join(str(v) for v in s)


class Genotype(object):

    def __init__(self, variant, sample_name, gt):
        self.format = dict()
        self.variant = variant
        self.set_format('GT', gt)

    def set_format(self, field, value):
        if field in [i.id for i in self.variant.format_list]:
            self.format[field] = value
            if field not in self.variant.active_formats:
                self.variant.active_formats.append(field)
                self.variant.active_formats.sort(key=lambda x: [f.id for f in
                    self.variant.format_list].index(x))
        else:
            sys.stderr.write('\nError: invalid FORMAT field, "' + field + '"\n'
                )
            exit(1)

    def get_format(self, field):
        return self.format[field]

    def get_gt_string(self):
        g_list = list()
        for f in self.variant.active_formats:
            if f in self.format:
                if type(self.format[f]) == float:
                    g_list.append('%0.2f' % self.format[f])
                else:
                    g_list.append(self.format[f])
            else:
                g_list.append('.')
        return ':'.join([str(s) for s in g_list])


def vcfToBedpe(vcf_file, bedpe_out):
    vcf = Vcf()
    in_header = True
    header = []
    unmatched = dict()
    for line in vcf_file:
        if in_header:
            if line[0] == '#':
                header.append(line)
                if line[1] != '#':
                    sample_list = line.rstrip().split('\t')[9:]
                continue
            else:
                bedpe_out.write('\t'.join(['#CHROM_A', 'START_A', 'END_A',
                    'CHROM_B', 'START_B', 'END_B', 'ID', 'QUAL', 'STRAND_A',
                    'STRAND_B', 'TYPE', 'FILTER', 'INFO', 'FORMAT'] +
                    sample_list) + '\n')
                in_header = False
                vcf.add_header(header)
        v = line.rstrip().split('\t')
        var = Variant(v, vcf)
        if var.info['SVTYPE'] != 'BND':
            b1 = var.pos
            b2 = int(var.info['END'])
            name = v[2]
            score = v[5]
            strands = var.info['STRANDS']
            o1 = strands[0]
            o2 = strands[1]
            span = [int(i) for i in var.info['CIPOS'].split(',')]
            s1 = b1 + span[0] - 1
            e1 = b1 + span[1]
            span = [int(i) for i in var.info['CIEND'].split(',')]
            s2 = b2 + span[0] - 1
            e2 = b2 + span[1]
            ispan = s2 - e1
            ospan = e2 - s1
            ev_list = list()
            for ev in ['PE', 'SR']:
                if int(var.info[ev]) > 0:
                    ev_list.append(ev)
            evtype = ','.join(ev_list)
            format_list = v[8].split(':')
            sample_gt = dict()
            var_sample_list = []
            for i in range(len(sample_list)):
                s = sample_list[i]
                gt = v[9 + i]
                format_dict = dict(zip(format_list, gt.split(':')))
                format_dict['PE'] = int(format_dict['PE'])
                format_dict['SR'] = int(format_dict['SR'])
                format_dict['SU'] = int(format_dict['SU'])
                if format_dict['SU'] > 0:
                    var_sample_list.append(sample_list[i])
                sample_gt[s] = format_dict
            gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in
                sample_list])
            support = sum([sample_gt[s]['SU'] for s in sample_list])
            bed_l = [var.chrom, s1, e1, var.chrom, s2, e2, name, var.qual,
                o1, o2, var.info['SVTYPE'], var.filter, var.get_info_string
                (), var.get_format_string()]
            bedpe_out.write('\t'.join(str(s) for s in bed_l + [var.gts[
                sample].get_gt_string() for sample in var.sample_list]) + '\n')
        else:
            mate_id = var.info['MATEID']
            if mate_id in unmatched:
                prim = unmatched[mate_id]
                sec = var
                b1 = prim.pos
                b2 = sec.pos
                score = v[5]
                strands = prim.info['STRANDS']
                o1 = strands[0]
                o2 = strands[1]
                span = [int(i) for i in prim.info['CIPOS'].split(',')]
                s1 = b1 + span[0] - 1
                e1 = b1 + span[1]
                span = [int(i) for i in sec.info['CIPOS'].split(',')]
                s2 = b2 + span[0] - 1
                e2 = b2 + span[1]
                ispan = s2 - e1
                ospan = e2 - s1
                ev_list = list()
                for ev in ['PE', 'SR']:
                    if int(var.info[ev]) > 0:
                        ev_list.append(ev)
                evtype = ','.join(ev_list)
                format_list = v[8].split(':')
                sample_gt = dict()
                var_sample_list = []
                for i in range(len(sample_list)):
                    s = sample_list[i]
                    gt = v[9 + i]
                    format_dict = dict(zip(format_list, gt.split(':')))
                    format_dict['PE'] = int(format_dict['PE'])
                    format_dict['SR'] = int(format_dict['SR'])
                    format_dict['SU'] = int(format_dict['SU'])
                    if format_dict['SU'] > 0:
                        var_sample_list.append(sample_list[i])
                    sample_gt[s] = format_dict
                gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in
                    sample_list])
                support = sum([sample_gt[s]['SU'] for s in sample_list])
                bed_l = [prim.chrom, s1, e1, sec.chrom, s2, e2, prim.info[
                    'EVENT'], prim.qual, o1, o2, prim.info['SVTYPE'], prim.
                    filter, prim.get_info_string(), prim.get_format_string(
                    ), '\t'.join([prim.gts[sample].get_gt_string() for
                    sample in prim.sample_list])]
                bedpe_out.write('\t'.join([str(s) for s in bed_l]) + '\n')
                del unmatched[mate_id]
            else:
                unmatched[var.var_id] = var
    if len(unmatched) > 0:
        sys.stderr.write('Warning: %s unmatched variants\n' % len(unmatched))
    bedpe_out.close()
    vcf_file.close()
    return


<mask token>

<mask token>


def get_args():
    parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter,
        description="""vcfToBedpe
author: """ + __author__ + '\nversion: ' +
        __version__ + """
description: Convert a VCF file to a BEDPE file""")
    parser.add_argument('-i', '--input', type=argparse.FileType('r'),
        default=None, help='VCF input (default: stdin)')
    parser.add_argument('-o', '--output', type=argparse.FileType('w'),
        default=sys.stdout, help='Output BEDPE to write (default: stdout)')
    args = parser.parse_args()
    if args.input == None:
        if sys.stdin.isatty():
            parser.print_help()
            exit(1)
        else:
            args.input = sys.stdin
    return args


class Vcf(object):

    def __init__(self):
        self.file_format = 'VCFv4.2'
        self.reference = ''
        self.sample_list = []
        self.info_list = []
        self.format_list = []
        self.alt_list = []
        self.add_format('GT', 1, 'String', 'Genotype')

    def add_header(self, header):
        for line in header:
            if line.split('=')[0] == '##fileformat':
                self.file_format = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##reference':
                self.reference = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##INFO':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_info(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##ALT':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_alt(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##FORMAT':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_format(*[b.split('=')[1] for b in r.findall(a)])
            elif line[0] == '#' and line[1] != '#':
                self.sample_list = line.rstrip().split('\t')[9:]

    def get_header(self):
        header = '\n'.join(['##fileformat=' + self.file_format, 
            '##fileDate=' + time.strftime('%Y%m%d'), '##reference=' + self.
            reference] + [i.hstring for i in self.info_list] + [a.hstring for
            a in self.alt_list] + [f.hstring for f in self.format_list] + [
            '\t'.join(['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL',
            'FILTER', 'INFO', 'FORMAT'] + self.sample_list)])
        return header

    def add_info(self, id, number, type, desc):
        if id not in [i.id for i in self.info_list]:
            inf = Info(id, number, type, desc)
            self.info_list.append(inf)

    def add_alt(self, id, desc):
        if id not in [a.id for a in self.alt_list]:
            alt = Alt(id, desc)
            self.alt_list.append(alt)

    def add_format(self, id, number, type, desc):
        if id not in [f.id for f in self.format_list]:
            fmt = Format(id, number, type, desc)
            self.format_list.append(fmt)

    def add_sample(self, name):
        self.sample_list.append(name)


class Info(object):

    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##INFO=<ID=' + self.id + ',Number=' + self.number +
            ',Type=' + self.type + ',Description="' + self.desc + '">')


class Alt(object):

    def __init__(self, id, desc):
        self.id = str(id)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##ALT=<ID=' + self.id + ',Description="' + self.
            desc + '">')


class Format(object):

    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##FORMAT=<ID=' + self.id + ',Number=' + self.
            number + ',Type=' + self.type + ',Description="' + self.desc + '">'
            )


class Variant(object):

    def __init__(self, var_list, vcf):
        self.chrom = var_list[0]
        self.pos = int(var_list[1])
        self.var_id = var_list[2]
        self.ref = var_list[3]
        self.alt = var_list[4]
        self.qual = var_list[5]
        self.filter = var_list[6]
        self.sample_list = vcf.sample_list
        self.info_list = vcf.info_list
        self.info = dict()
        self.format_list = vcf.format_list
        self.active_formats = list()
        self.gts = dict()
        for i in range(len(self.sample_list)):
            s_gt = var_list[9 + i].split(':')[0]
            s = self.sample_list[i]
            self.gts[s] = Genotype(self, s, s_gt)
        for i in range(len(self.sample_list)):
            s = self.sample_list[i]
            for j in zip(var_list[8].split(':'), var_list[9 + i].split(':')):
                self.gts[s].set_format(j[0], j[1])
        self.info = dict()
        i_split = [a.split('=') for a in var_list[7].split(';')]
        for i in i_split:
            if len(i) == 1:
                i.append(True)
            self.info[i[0]] = i[1]

    def set_info(self, field, value):
        if field in [i.id for i in self.info_list]:
            self.info[field] = value
        else:
            sys.stderr.write('\nError: invalid INFO field, "' + field + '"\n')
            exit(1)

    def get_info(self, field):
        return self.info[field]

    def get_info_string(self):
        i_list = list()
        for info_field in self.info_list:
            if info_field.id in self.info:
                if info_field.type == 'Flag':
                    i_list.append(info_field.id)
                else:
                    i_list.append('%s=%s' % (info_field.id, self.info[
                        info_field.id]))
        return ';'.join(i_list)

    def get_format_string(self):
        f_list = list()
        for f in self.format_list:
            if f.id in self.active_formats:
                f_list.append(f.id)
        return ':'.join(f_list)

    def genotype(self, sample_name):
        if sample_name in self.sample_list:
            return self.gts[sample_name]
        else:
            sys.stderr.write('\nError: invalid sample name, "' +
                sample_name + '"\n')

    def get_var_string(self):
        s = [self.chrom, self.pos, self.var_id, self.ref, self.alt, '%0.2f' %
            self.qual, self.filter, self.get_info_string(), self.
            get_format_string(), '\t'.join(self.genotype(s).get_gt_string() for
            s in self.sample_list)]
        return '\t'.join(str(v) for v in s)


class Genotype(object):

    def __init__(self, variant, sample_name, gt):
        self.format = dict()
        self.variant = variant
        self.set_format('GT', gt)

    def set_format(self, field, value):
        if field in [i.id for i in self.variant.format_list]:
            self.format[field] = value
            if field not in self.variant.active_formats:
                self.variant.active_formats.append(field)
                self.variant.active_formats.sort(key=lambda x: [f.id for f in
                    self.variant.format_list].index(x))
        else:
            sys.stderr.write('\nError: invalid FORMAT field, "' + field + '"\n'
                )
            exit(1)

    def get_format(self, field):
        return self.format[field]

    def get_gt_string(self):
        g_list = list()
        for f in self.variant.active_formats:
            if f in self.format:
                if type(self.format[f]) == float:
                    g_list.append('%0.2f' % self.format[f])
                else:
                    g_list.append(self.format[f])
            else:
                g_list.append('.')
        return ':'.join([str(s) for s in g_list])


def vcfToBedpe(vcf_file, bedpe_out):
    vcf = Vcf()
    in_header = True
    header = []
    unmatched = dict()
    for line in vcf_file:
        if in_header:
            if line[0] == '#':
                header.append(line)
                if line[1] != '#':
                    sample_list = line.rstrip().split('\t')[9:]
                continue
            else:
                bedpe_out.write('\t'.join(['#CHROM_A', 'START_A', 'END_A',
                    'CHROM_B', 'START_B', 'END_B', 'ID', 'QUAL', 'STRAND_A',
                    'STRAND_B', 'TYPE', 'FILTER', 'INFO', 'FORMAT'] +
                    sample_list) + '\n')
                in_header = False
                vcf.add_header(header)
        v = line.rstrip().split('\t')
        var = Variant(v, vcf)
        if var.info['SVTYPE'] != 'BND':
            b1 = var.pos
            b2 = int(var.info['END'])
            name = v[2]
            score = v[5]
            strands = var.info['STRANDS']
            o1 = strands[0]
            o2 = strands[1]
            span = [int(i) for i in var.info['CIPOS'].split(',')]
            s1 = b1 + span[0] - 1
            e1 = b1 + span[1]
            span = [int(i) for i in var.info['CIEND'].split(',')]
            s2 = b2 + span[0] - 1
            e2 = b2 + span[1]
            ispan = s2 - e1
            ospan = e2 - s1
            ev_list = list()
            for ev in ['PE', 'SR']:
                if int(var.info[ev]) > 0:
                    ev_list.append(ev)
            evtype = ','.join(ev_list)
            format_list = v[8].split(':')
            sample_gt = dict()
            var_sample_list = []
            for i in range(len(sample_list)):
                s = sample_list[i]
                gt = v[9 + i]
                format_dict = dict(zip(format_list, gt.split(':')))
                format_dict['PE'] = int(format_dict['PE'])
                format_dict['SR'] = int(format_dict['SR'])
                format_dict['SU'] = int(format_dict['SU'])
                if format_dict['SU'] > 0:
                    var_sample_list.append(sample_list[i])
                sample_gt[s] = format_dict
            gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in
                sample_list])
            support = sum([sample_gt[s]['SU'] for s in sample_list])
            bed_l = [var.chrom, s1, e1, var.chrom, s2, e2, name, var.qual,
                o1, o2, var.info['SVTYPE'], var.filter, var.get_info_string
                (), var.get_format_string()]
            bedpe_out.write('\t'.join(str(s) for s in bed_l + [var.gts[
                sample].get_gt_string() for sample in var.sample_list]) + '\n')
        else:
            mate_id = var.info['MATEID']
            if mate_id in unmatched:
                prim = unmatched[mate_id]
                sec = var
                b1 = prim.pos
                b2 = sec.pos
                score = v[5]
                strands = prim.info['STRANDS']
                o1 = strands[0]
                o2 = strands[1]
                span = [int(i) for i in prim.info['CIPOS'].split(',')]
                s1 = b1 + span[0] - 1
                e1 = b1 + span[1]
                span = [int(i) for i in sec.info['CIPOS'].split(',')]
                s2 = b2 + span[0] - 1
                e2 = b2 + span[1]
                ispan = s2 - e1
                ospan = e2 - s1
                ev_list = list()
                for ev in ['PE', 'SR']:
                    if int(var.info[ev]) > 0:
                        ev_list.append(ev)
                evtype = ','.join(ev_list)
                format_list = v[8].split(':')
                sample_gt = dict()
                var_sample_list = []
                for i in range(len(sample_list)):
                    s = sample_list[i]
                    gt = v[9 + i]
                    format_dict = dict(zip(format_list, gt.split(':')))
                    format_dict['PE'] = int(format_dict['PE'])
                    format_dict['SR'] = int(format_dict['SR'])
                    format_dict['SU'] = int(format_dict['SU'])
                    if format_dict['SU'] > 0:
                        var_sample_list.append(sample_list[i])
                    sample_gt[s] = format_dict
                gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in
                    sample_list])
                support = sum([sample_gt[s]['SU'] for s in sample_list])
                bed_l = [prim.chrom, s1, e1, sec.chrom, s2, e2, prim.info[
                    'EVENT'], prim.qual, o1, o2, prim.info['SVTYPE'], prim.
                    filter, prim.get_info_string(), prim.get_format_string(
                    ), '\t'.join([prim.gts[sample].get_gt_string() for
                    sample in prim.sample_list])]
                bedpe_out.write('\t'.join([str(s) for s in bed_l]) + '\n')
                del unmatched[mate_id]
            else:
                unmatched[var.var_id] = var
    if len(unmatched) > 0:
        sys.stderr.write('Warning: %s unmatched variants\n' % len(unmatched))
    bedpe_out.close()
    vcf_file.close()
    return


def main():
    args = get_args()
    vcfToBedpe(args.input, args.output)


if __name__ == '__main__':
    try:
        sys.exit(main())
    except IOError as e:
        if e.errno != 32:
            raise

import argparse, sys
import math, time, re
from argparse import RawTextHelpFormatter
__author__ = 'Colby Chiang (cc2qe@virginia.edu)'
__version__ = '$Revision: 0.0.1 $'
__date__ = '$Date: 2014-04-23 14:31 $'


def get_args():
    parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter,
        description="""vcfToBedpe
author: """ + __author__ + '\nversion: ' +
        __version__ + """
description: Convert a VCF file to a BEDPE file""")
    parser.add_argument('-i', '--input', type=argparse.FileType('r'),
        default=None, help='VCF input (default: stdin)')
    parser.add_argument('-o', '--output', type=argparse.FileType('w'),
        default=sys.stdout, help='Output BEDPE to write (default: stdout)')
    args = parser.parse_args()
    if args.input == None:
        if sys.stdin.isatty():
            parser.print_help()
            exit(1)
        else:
            args.input = sys.stdin
    return args


class Vcf(object):

    def __init__(self):
        self.file_format = 'VCFv4.2'
        self.reference = ''
        self.sample_list = []
        self.info_list = []
        self.format_list = []
        self.alt_list = []
        self.add_format('GT', 1, 'String', 'Genotype')

    def add_header(self, header):
        for line in header:
            if line.split('=')[0] == '##fileformat':
                self.file_format = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##reference':
                self.reference = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##INFO':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_info(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##ALT':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_alt(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##FORMAT':
                a = line[line.find('<') + 1:line.find('>')]
                r = re.compile('(?:[^,\\"]|\\"[^\\"]*\\")+')
                self.add_format(*[b.split('=')[1] for b in r.findall(a)])
            elif line[0] == '#' and line[1] != '#':
                self.sample_list = line.rstrip().split('\t')[9:]

    def get_header(self):
        header = '\n'.join(['##fileformat=' + self.file_format, 
            '##fileDate=' + time.strftime('%Y%m%d'), '##reference=' + self.
            reference] + [i.hstring for i in self.info_list] + [a.hstring for
            a in self.alt_list] + [f.hstring for f in self.format_list] + [
            '\t'.join(['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL',
            'FILTER', 'INFO', 'FORMAT'] + self.sample_list)])
        return header

    def add_info(self, id, number, type, desc):
        if id not in [i.id for i in self.info_list]:
            inf = Info(id, number, type, desc)
            self.info_list.append(inf)

    def add_alt(self, id, desc):
        if id not in [a.id for a in self.alt_list]:
            alt = Alt(id, desc)
            self.alt_list.append(alt)

    def add_format(self, id, number, type, desc):
        if id not in [f.id for f in self.format_list]:
            fmt = Format(id, number, type, desc)
            self.format_list.append(fmt)

    def add_sample(self, name):
        self.sample_list.append(name)


class Info(object):

    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##INFO=<ID=' + self.id + ',Number=' + self.number +
            ',Type=' + self.type + ',Description="' + self.desc + '">')


class Alt(object):

    def __init__(self, id, desc):
        self.id = str(id)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##ALT=<ID=' + self.id + ',Description="' + self.
            desc + '">')


class Format(object):

    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = ('##FORMAT=<ID=' + self.id + ',Number=' + self.
            number + ',Type=' + self.type + ',Description="' + self.desc + '">'
            )


class Variant(object):

    def __init__(self, var_list, vcf):
        self.chrom = var_list[0]
        self.pos = int(var_list[1])
        self.var_id = var_list[2]
        self.ref = var_list[3]
        self.alt = var_list[4]
        self.qual = var_list[5]
        self.filter = var_list[6]
        self.sample_list = vcf.sample_list
        self.info_list = vcf.info_list
        self.info = dict()
        self.format_list = vcf.format_list
        self.active_formats = list()
        self.gts = dict()
        for i in range(len(self.sample_list)):
            s_gt = var_list[9 + i].split(':')[0]
            s = self.sample_list[i]
            self.gts[s] = Genotype(self, s, s_gt)
        for i in range(len(self.sample_list)):
            s = self.sample_list[i]
            for j in zip(var_list[8].split(':'), var_list[9 + i].split(':')):
                self.gts[s].set_format(j[0], j[1])
        self.info = dict()
        i_split = [a.split('=') for a in var_list[7].split(';')]
        for i in i_split:
            if len(i) == 1:
                i.append(True)
            self.info[i[0]] = i[1]

    def set_info(self, field, value):
        if field in [i.id for i in self.info_list]:
            self.info[field] = value
        else:
            sys.stderr.write('\nError: invalid INFO field, "' + field + '"\n')
            exit(1)

    def get_info(self, field):
        return self.info[field]

    def get_info_string(self):
        i_list = list()
        for info_field in self.info_list:
            if info_field.id in self.info:
                if info_field.type == 'Flag':
                    i_list.append(info_field.id)
                else:
                    i_list.append('%s=%s' % (info_field.id, self.info[
                        info_field.id]))
        return ';'.join(i_list)

    def get_format_string(self):
        f_list = list()
        for f in self.format_list:
            if f.id in self.active_formats:
                f_list.append(f.id)
        return ':'.join(f_list)

    def genotype(self, sample_name):
        if sample_name in self.sample_list:
            return self.gts[sample_name]
        else:
            sys.stderr.write('\nError: invalid sample name, "' +
                sample_name + '"\n')

    def get_var_string(self):
        s = [self.chrom, self.pos, self.var_id, self.ref, self.alt, '%0.2f' %
            self.qual, self.filter, self.get_info_string(), self.
            get_format_string(), '\t'.join(self.genotype(s).get_gt_string() for
            s in self.sample_list)]
        return '\t'.join(str(v) for v in s)


class Genotype(object):

    def __init__(self, variant, sample_name, gt):
        self.format = dict()
        self.variant = variant
        self.set_format('GT', gt)

    def set_format(self, field, value):
        if field in [i.id for i in self.variant.format_list]:
            self.format[field] = value
            if field not in self.variant.active_formats:
                self.variant.active_formats.append(field)
                self.variant.active_formats.sort(key=lambda x: [f.id for f in
                    self.variant.format_list].index(x))
        else:
            sys.stderr.write('\nError: invalid FORMAT field, "' + field + '"\n'
                )
            exit(1)

    def get_format(self, field):
        return self.format[field]

    def get_gt_string(self):
        g_list = list()
        for f in self.variant.active_formats:
            if f in self.format:
                if type(self.format[f]) == float:
                    g_list.append('%0.2f' % self.format[f])
                else:
                    g_list.append(self.format[f])
            else:
                g_list.append('.')
        return ':'.join([str(s) for s in g_list])


def vcfToBedpe(vcf_file, bedpe_out):
    vcf = Vcf()
    in_header = True
    header = []
    unmatched = dict()
    for line in vcf_file:
        if in_header:
            if line[0] == '#':
                header.append(line)
                if line[1] != '#':
                    sample_list = line.rstrip().split('\t')[9:]
                continue
            else:
                bedpe_out.write('\t'.join(['#CHROM_A', 'START_A', 'END_A',
                    'CHROM_B', 'START_B', 'END_B', 'ID', 'QUAL', 'STRAND_A',
                    'STRAND_B', 'TYPE', 'FILTER', 'INFO', 'FORMAT'] +
                    sample_list) + '\n')
                in_header = False
                vcf.add_header(header)
        v = line.rstrip().split('\t')
        var = Variant(v, vcf)
        if var.info['SVTYPE'] != 'BND':
            b1 = var.pos
            b2 = int(var.info['END'])
            name = v[2]
            score = v[5]
            strands = var.info['STRANDS']
            o1 = strands[0]
            o2 = strands[1]
            span = [int(i) for i in var.info['CIPOS'].split(',')]
            s1 = b1 + span[0] - 1
            e1 = b1 + span[1]
            span = [int(i) for i in var.info['CIEND'].split(',')]
            s2 = b2 + span[0] - 1
            e2 = b2 + span[1]
            ispan = s2 - e1
            ospan = e2 - s1
            ev_list = list()
            for ev in ['PE', 'SR']:
                if int(var.info[ev]) > 0:
                    ev_list.append(ev)
            evtype = ','.join(ev_list)
            format_list = v[8].split(':')
            sample_gt = dict()
            var_sample_list = []
            for i in range(len(sample_list)):
                s = sample_list[i]
                gt = v[9 + i]
                format_dict = dict(zip(format_list, gt.split(':')))
                format_dict['PE'] = int(format_dict['PE'])
                format_dict['SR'] = int(format_dict['SR'])
                format_dict['SU'] = int(format_dict['SU'])
                if format_dict['SU'] > 0:
                    var_sample_list.append(sample_list[i])
                sample_gt[s] = format_dict
            gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in
                sample_list])
            support = sum([sample_gt[s]['SU'] for s in sample_list])
            bed_l = [var.chrom, s1, e1, var.chrom, s2, e2, name, var.qual,
                o1, o2, var.info['SVTYPE'], var.filter, var.get_info_string
                (), var.get_format_string()]
            bedpe_out.write('\t'.join(str(s) for s in bed_l + [var.gts[
                sample].get_gt_string() for sample in var.sample_list]) + '\n')
        else:
            mate_id = var.info['MATEID']
            if mate_id in unmatched:
                prim = unmatched[mate_id]
                sec = var
                b1 = prim.pos
                b2 = sec.pos
                score = v[5]
                strands = prim.info['STRANDS']
                o1 = strands[0]
                o2 = strands[1]
                span = [int(i) for i in prim.info['CIPOS'].split(',')]
                s1 = b1 + span[0] - 1
                e1 = b1 + span[1]
                span = [int(i) for i in sec.info['CIPOS'].split(',')]
                s2 = b2 + span[0] - 1
                e2 = b2 + span[1]
                ispan = s2 - e1
                ospan = e2 - s1
                ev_list = list()
                for ev in ['PE', 'SR']:
                    if int(var.info[ev]) > 0:
                        ev_list.append(ev)
                evtype = ','.join(ev_list)
                format_list = v[8].split(':')
                sample_gt = dict()
                var_sample_list = []
                for i in range(len(sample_list)):
                    s = sample_list[i]
                    gt = v[9 + i]
                    format_dict = dict(zip(format_list, gt.split(':')))
                    format_dict['PE'] = int(format_dict['PE'])
                    format_dict['SR'] = int(format_dict['SR'])
                    format_dict['SU'] = int(format_dict['SU'])
                    if format_dict['SU'] > 0:
                        var_sample_list.append(sample_list[i])
                    sample_gt[s] = format_dict
                gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in
                    sample_list])
                support = sum([sample_gt[s]['SU'] for s in sample_list])
                bed_l = [prim.chrom, s1, e1, sec.chrom, s2, e2, prim.info[
                    'EVENT'], prim.qual, o1, o2, prim.info['SVTYPE'], prim.
                    filter, prim.get_info_string(), prim.get_format_string(
                    ), '\t'.join([prim.gts[sample].get_gt_string() for
                    sample in prim.sample_list])]
                bedpe_out.write('\t'.join([str(s) for s in bed_l]) + '\n')
                del unmatched[mate_id]
            else:
                unmatched[var.var_id] = var
    if len(unmatched) > 0:
        sys.stderr.write('Warning: %s unmatched variants\n' % len(unmatched))
    bedpe_out.close()
    vcf_file.close()
    return


def main():
    args = get_args()
    vcfToBedpe(args.input, args.output)


if __name__ == '__main__':
    try:
        sys.exit(main())
    except IOError as e:
        if e.errno != 32:
            raise

#!/usr/bin/env python

import argparse, sys
import math, time, re
from argparse import RawTextHelpFormatter

__author__ = "Colby Chiang (cc2qe@virginia.edu)"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2014-04-23 14:31 $"

# --------------------------------------
# define functions

def get_args():
    parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter, description="\
vcfToBedpe\n\
author: " + __author__ + "\n\
version: " + __version__ + "\n\
description: Convert a VCF file to a BEDPE file")
    parser.add_argument('-i', '--input', type=argparse.FileType('r'), default=None, help='VCF input (default: stdin)')
    parser.add_argument('-o', '--output', type=argparse.FileType('w'), default=sys.stdout, help='Output BEDPE to write (default: stdout)')

    # parse the arguments
    args = parser.parse_args()

    # if no input, check if part of pipe and if so, read stdin.
    if args.input == None:
        if sys.stdin.isatty():
            parser.print_help()
            exit(1)
        else:
            args.input = sys.stdin

    # send back the user input
    return args

class Vcf(object):
    def __init__(self):
        self.file_format = 'VCFv4.2'
        # self.fasta = fasta
        self.reference = ''
        self.sample_list = []
        self.info_list = []
        self.format_list = []
        self.alt_list = []
        self.add_format('GT', 1, 'String', 'Genotype')

    def add_header(self, header):
        for line in header:
            if line.split('=')[0] == '##fileformat':
                self.file_format = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##reference':
                self.reference = line.rstrip().split('=')[1]
            elif line.split('=')[0] == '##INFO':
                a = line[line.find('<')+1:line.find('>')]
                r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+')
                self.add_info(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##ALT':
                a = line[line.find('<')+1:line.find('>')]
                r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+')
                self.add_alt(*[b.split('=')[1] for b in r.findall(a)])
            elif line.split('=')[0] == '##FORMAT':
                a = line[line.find('<')+1:line.find('>')]
                r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+')
                self.add_format(*[b.split('=')[1] for b in r.findall(a)])
            elif line[0] == '#' and line[1] != '#':
                self.sample_list = line.rstrip().split('\t')[9:]
    # return the VCF header
    def get_header(self):
        header = '\n'.join(['##fileformat=' + self.file_format,
                            '##fileDate=' + time.strftime('%Y%m%d'),
                            '##reference=' + self.reference] + \
                           [i.hstring for i in self.info_list] + \
                           [a.hstring for a in self.alt_list] + \
                           [f.hstring for f in self.format_list] + \
                           ['\t'.join([
                               '#CHROM',
                               'POS',
                               'ID',
                               'REF',
                               'ALT',
                               'QUAL',
                               'FILTER',
                               'INFO',
                               'FORMAT'] + \
                                      self.sample_list
                                  )])
        return header

    def add_info(self, id, number, type, desc):
        if id not in [i.id for i in self.info_list]:
            inf = Info(id, number, type, desc)
            self.info_list.append(inf)

    def add_alt(self, id, desc):
        if id not in [a.id for a in self.alt_list]:
            alt = Alt(id, desc)
            self.alt_list.append(alt)

    def add_format(self, id, number, type, desc):
        if id not in [f.id for f in self.format_list]:
            fmt = Format(id, number, type, desc)
            self.format_list.append(fmt)

    def add_sample(self, name):
        self.sample_list.append(name)

class Info(object):
    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        # strip the double quotes around the string if present
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = '##INFO=<ID=' + self.id + ',Number=' + self.number + ',Type=' + self.type + ',Description=\"' + self.desc + '\">'

class Alt(object):
    def __init__(self, id, desc):
        self.id = str(id)
        self.desc = str(desc)
        # strip the double quotes around the string if present
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = '##ALT=<ID=' + self.id + ',Description=\"' + self.desc + '\">'

class Format(object):
    def __init__(self, id, number, type, desc):
        self.id = str(id)
        self.number = str(number)
        self.type = str(type)
        self.desc = str(desc)
        # strip the double quotes around the string if present
        if self.desc.startswith('"') and self.desc.endswith('"'):
            self.desc = self.desc[1:-1]
        self.hstring = '##FORMAT=<ID=' + self.id + ',Number=' + self.number + ',Type=' + self.type + ',Description=\"' + self.desc + '\">'

class Variant(object):
    def __init__(self, var_list, vcf):
        self.chrom = var_list[0]
        self.pos = int(var_list[1])
        self.var_id = var_list[2]
        self.ref = var_list[3]
        self.alt = var_list[4]
        self.qual = var_list[5]
        self.filter = var_list[6]
        self.sample_list = vcf.sample_list
        self.info_list = vcf.info_list
        self.info = dict()
        self.format_list = vcf.format_list
        self.active_formats = list()
        self.gts = dict()
        # make a genotype for each sample at variant
        for i in range(len(self.sample_list)):
            s_gt = var_list[9+i].split(':')[0]
            s = self.sample_list[i]
            self.gts[s] = Genotype(self, s, s_gt)
        # import the existing fmt fields
        for i in range(len(self.sample_list)):
            s = self.sample_list[i]
            for j in zip(var_list[8].split(':'), var_list[9+i].split(':')):
                self.gts[s].set_format(j[0], j[1])

        self.info = dict()
        i_split = [a.split('=') for a in var_list[7].split(';')] # temp list of split info column
        for i in i_split:
            if len(i) == 1:
                i.append(True)
            self.info[i[0]] = i[1]

    def set_info(self, field, value):
        if field in [i.id for i in self.info_list]:
            self.info[field] = value
        else:
            sys.stderr.write('\nError: invalid INFO field, \"' + field + '\"\n')
            exit(1)

    def get_info(self, field):
        return self.info[field]

    def get_info_string(self):
        i_list = list()
        for info_field in self.info_list:
            if info_field.id in self.info:
                if info_field.type == 'Flag':
                    i_list.append(info_field.id)
                else:
                    i_list.append('%s=%s' % (info_field.id, self.info[info_field.id]))
        return ';'.join(i_list)

    def get_format_string(self):
        f_list = list()
        for f in self.format_list:
            if f.id in self.active_formats:
                f_list.append(f.id)
        return ':'.join(f_list)

    def genotype(self, sample_name):
        if sample_name in self.sample_list:
            return self.gts[sample_name]
        else:
            sys.stderr.write('\nError: invalid sample name, \"' + sample_name + '\"\n')

    def get_var_string(self):
        s =[
            self.chrom,
            self.pos,
            self.var_id,
            self.ref,
            self.alt,
            '%0.2f' % self.qual,
            self.filter,
            self.get_info_string(),
            self.get_format_string(),
            '\t'.join(self.genotype(s).get_gt_string() for s in self.sample_list)
        ]
        return '\t'.join(str(v) for v in s)

class Genotype(object):
    def __init__(self, variant, sample_name, gt):
        self.format = dict()
        self.variant = variant
        self.set_format('GT', gt)

    def set_format(self, field, value):
        if field in [i.id for i in self.variant.format_list]:
            self.format[field] = value
            if field not in self.variant.active_formats:
                self.variant.active_formats.append(field)
                # sort it to be in the same order as the format_list in header
                self.variant.active_formats.sort(key=lambda x: [f.id for f in self.variant.format_list].index(x))
        else:
            sys.stderr.write('\nError: invalid FORMAT field, \"' + field + '\"\n')
            exit(1)

    def get_format(self, field):
        return self.format[field]

    def get_gt_string(self):
        g_list = list()
        for f in self.variant.active_formats:
            if f in self.format:
                if type(self.format[f]) == float:
                    g_list.append('%0.2f' % self.format[f])
                else:
                    g_list.append(self.format[f])
            else:
                g_list.append('.')
        return ':'.join([str(s) for s in g_list])

# primary function
def vcfToBedpe(vcf_file, bedpe_out):
    vcf = Vcf()
    in_header = True
    header = []
    # dict of BND variant lines that have not yet been matched.
    # variant id is the key
    unmatched = dict()

    for line in vcf_file:
        if in_header:
            if line[0] == '#':
                header.append(line)
                if line[1] != '#':
                    sample_list = line.rstrip().split('\t')[9:]
                continue
            else:
                # print header
                bedpe_out.write('\t'.join(['#CHROM_A',
                                           'START_A',
                                           'END_A',
                                           'CHROM_B',
                                           'START_B',
                                           'END_B',
                                           'ID',
                                           'QUAL',
                                           'STRAND_A',
                                           'STRAND_B',
                                           'TYPE',
                                           'FILTER',
                                           'INFO',
                                           'FORMAT'] +
                                           sample_list
                                          ) + '\n')
                in_header = False
                vcf.add_header(header)

        v = line.rstrip().split('\t')
        var = Variant(v, vcf)

        if var.info['SVTYPE'] != 'BND':
            b1 = var.pos
            b2 = int(var.info['END'])
            name = v[2]
            score = v[5]

            strands = var.info['STRANDS']
            o1 = strands[0]
            o2 = strands[1]

            span = [int(i) for i in var.info['CIPOS'].split(',')]
            s1 = b1 + span[0] - 1
            e1 = b1 + span[1]

            span = [int(i) for i in var.info['CIEND'].split(',')]
            s2 = b2 + span[0] - 1
            e2 = b2 + span[1]

            ispan = s2 - e1
            ospan = e2 - s1

            ev_list = list()
            for ev in ['PE', 'SR']:
                if int(var.info[ev]) > 0:
                    ev_list.append(ev)
            evtype = ','.join(ev_list)

            format_list = v[8].split(':')
            sample_gt = dict()
            var_sample_list = []
            for i in range(len(sample_list)):
                s = sample_list[i]
                gt = v[9 + i]
                format_dict = dict(zip(format_list, gt.split(':')))
                format_dict['PE'] = int(format_dict['PE'])
                format_dict['SR'] = int(format_dict['SR'])
                format_dict['SU'] = int(format_dict['SU'])
                if format_dict['SU'] > 0:
                    var_sample_list.append(sample_list[i])
                sample_gt[s] = format_dict

            gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in sample_list])
            support = sum([sample_gt[s]['SU'] for s in sample_list])

            bed_l =[var.chrom,
                    s1,
                    e1,
                    var.chrom,
                    s2,
                    e2,
                    name,
                    var.qual,
                    o1,
                    o2,
                    var.info['SVTYPE'],
                    var.filter,
                    var.get_info_string(),
                    var.get_format_string()]
            bedpe_out.write('\t'.join(str(s) for s in bed_l + [var.gts[sample].get_gt_string() for sample in var.sample_list]) + '\n')

        else:
            mate_id = var.info['MATEID']
            if mate_id in unmatched:
                prim = unmatched[mate_id]
                sec = var

                b1 = prim.pos
                b2 = sec.pos
                score = v[5]

                strands = prim.info['STRANDS']
                o1 = strands[0]
                o2 = strands[1]

                span = [int(i) for i in prim.info['CIPOS'].split(',')]
                s1 = b1 + span[0] - 1
                e1 = b1 + span[1]

                span = [int(i) for i in sec.info['CIPOS'].split(',')]
                s2 = b2 + span[0] - 1
                e2 = b2 + span[1]

                ispan = s2 - e1
                ospan = e2 - s1

                ev_list = list()
                for ev in ['PE', 'SR']:
                    if int(var.info[ev]) > 0:
                        ev_list.append(ev)
                evtype = ','.join(ev_list)

                format_list = v[8].split(':')
                sample_gt = dict()
                var_sample_list = []
                for i in range(len(sample_list)):
                    s = sample_list[i]
                    gt = v[9 + i]
                    format_dict = dict(zip(format_list, gt.split(':')))
                    format_dict['PE'] = int(format_dict['PE'])
                    format_dict['SR'] = int(format_dict['SR'])
                    format_dict['SU'] = int(format_dict['SU'])
                    if format_dict['SU'] > 0:
                        var_sample_list.append(sample_list[i])
                    sample_gt[s] = format_dict

                gt_string = '\t'.join([str(sample_gt[s]['SU']) for s in sample_list])
                support = sum([sample_gt[s]['SU'] for s in sample_list])

                bed_l = [prim.chrom,
                         s1,
                         e1,
                         sec.chrom,
                         s2,
                         e2,
                         prim.info['EVENT'],
                         prim.qual,
                         o1,
                         o2,
                         prim.info['SVTYPE'],
                         prim.filter,
                         prim.get_info_string(),
                         prim.get_format_string(),
                         '\t'.join([prim.gts[sample].get_gt_string() for sample in prim.sample_list])]
                bedpe_out.write('\t'.join([str(s) for s in bed_l]) + '\n')

                # delete the mate from the dictionary
                del unmatched[mate_id]
            else:
                # if the mate isn't already in the dict, add current variant to dictionary
                unmatched[var.var_id] = var

    if len(unmatched) > 0:
        sys.stderr.write("Warning: %s unmatched variants\n"
                         % len(unmatched))
    # close the files
    bedpe_out.close()
    vcf_file.close()

    return

# --------------------------------------
# wrapper function

def main():
    # parse the command line args
    args = get_args()

    # call primary function
    vcfToBedpe(args.input, args.output)

# initialize the script
if __name__ == '__main__':
    try:
        sys.exit(main())
    except IOError as e:
        if e.errno != 32:  # ignore SIGPIPE
            raise
