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annotate_rd.py
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#!/usr/bin/env python
import tempfile
import argparse, sys, os
import math, time, re
from argparse import RawTextHelpFormatter
from subprocess import Popen, PIPE, STDOUT
__author__ = "Colby Chiang ([email protected])"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2014-04-28 14:31 $"
# --------------------------------------
# define functions
def get_args():
parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter, description="\
svgt\n\
author: " + __author__ + "\n\
version: " + __version__ + "\n\
description: Compute genotype of structural variants based on breakpoint depth")
parser.add_argument('-v', '--input_vcf', type=argparse.FileType('r'), default=None, help='VCF input')
parser.add_argument('-s', '--sample', type=str, required=True, help='sample to annotate')
parser.add_argument('-r', '--root', type=str, required=True, help='CNVnator .root histogram file')
parser.add_argument('-o', '--output_vcf', type=argparse.FileType('w'), default=sys.stdout, help='output VCF to write (default: stdout)')
parser.add_argument('--debug', action='store_true', help='debugging verbosity')
# parse the arguments
args = parser.parse_args()
# if no input, check if part of pipe and if so, read stdin.
if args.input_vcf == None:
if sys.stdin.isatty():
parser.print_help()
exit(1)
else:
args.input_vcf = 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 = self.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 = self.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 = self.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 = float(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 xrange(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 xrange(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.keys():
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 = '\t'.join(map(str,[
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 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(map(str,g_list))
# primary function
def sv_genotype(vcf_file, sample, root, vcf_out, debug):
in_header = True
header = []
vcf = Vcf()
window = 100
# make 2 passes through the vcf file, because it's much faster to give a single
# command to CNVnator.
coord_list = tempfile.NamedTemporaryFile(dir='./', delete=False)
for line in vcf_file:
if in_header:
if line[0] == '#':
header.append(line)
if line[1] != '#':
vcf_samples = line.rstrip().split('\t')[9:]
continue
else:
in_header = False
vcf.add_header(header)
v = line.rstrip().split('\t')
var = Variant(v, vcf)
if var.get_info('SVTYPE') != 'BND':
end = var.get_info('END')
coord_list.write('%s:%s-%s\n' % (var.chrom, var.pos, end))
coord_list.write('exit\n')
coord_list.close()
p1 = Popen(['cat', coord_list.name], stdout=PIPE, stderr=STDOUT)
cmd = map(str, ['cnvnator', '-root', root, '-genotype', window])
p2 = Popen(cmd, stdin=p1.stdout, stdout=PIPE, stderr=STDOUT)
p3 = Popen(['awk', '{ print $4 }'], stdin=p2.stdout, stdout=PIPE, stderr=STDOUT)
cn_list = map(float, p3.communicate()[0].split('\n')[:-1])
# go through the VCF a second time and add the read depth annotations
vcf_file.seek(0)
in_header = True
header = []
vcf = Vcf()
i = 0
for line in vcf_file:
if in_header:
if line[0] == '#':
header.append(line)
if line[1] != '#':
vcf_samples = line.rstrip().split('\t')[9:]
continue
else:
in_header = False
vcf.add_header(header)
vcf.add_format('CN', 1, 'Float', 'Copy number of structural variant segment.')
vcf_out.write(vcf.get_header() + '\n')
v = line.rstrip().split('\t')
var = Variant(v, vcf)
if var.get_info('SVTYPE') != 'BND':
var.genotype(sample).set_format('CN', cn_list[i])
i += 1
# write the VCF
vcf_out.write(var.get_var_string() + '\n')
vcf_out.close()
# remove temp file
os.unlink(coord_list.name)
return
# --------------------------------------
# main function
def main():
# parse the command line args
args = get_args()
# call primary function
sv_genotype(args.input_vcf, args.sample, args.root, args.output_vcf, args.debug)
# close the files
args.input_vcf.close()
# initialize the script
if __name__ == '__main__':
try:
sys.exit(main())
except IOError, e:
if e.errno != 32: # ignore SIGPIPE
raise