wdecoster

from cyvcf2 import VCF, Writer
from pyfaidx import Fasta
from argparse import ArgumentParser


def main():
    args = get_args()
    genome = Fasta(args.genome)
    vcf = VCF(args.vcf)
    output = Writer(args.output, vcf)

wdecoster

from argparse import ArgumentParser
from Bio import SeqIO
import gzip
from dateutil.parser import parse as dparse


def main():
    args = get_args()
    time_from = dparse(args.time_from)
    time_to = dparse(args.time_to)

wdecoster

from cyvcf2 import VCF
from argparse import ArgumentParser
import matplotlib.pyplot as plt
import sys


def main():
    args = get_args()
    sample_dict = get_sample_dict(args.samples)
    vcf = VCF(args.vcf)

wdecoster

from apiclient.discovery import build
from httplib2 import Http
from oauth2client import file, client, tools
from time import time
from datetime import datetime


class Document(object):
    def __init__(self, title, id):
        """Title is free, id is google docs identifier"""

wdecoster

from apiclient.discovery import build
from httplib2 import Http
from oauth2client import file, client, tools
from time import time
from datetime import datetime


def main():
    service = setup_api()
    file_ids = get_files_in_folder(service, folder_id="folder_id")

wdecoster

from cyvcf2 import VCF
import sys
import matplotlib.pyplot as plt
from matplotlib_venn import venn2


def is_variant(call):
    if call == 1 or call == 3:
        return True
    else:

wdecoster

chromosome	begin	end	name	outer_begin	outer_end	strand	primer1	primer2	numamplicons	amplicons	primer1_hits	primer1_snpsmaxfreq	primer1_snps	primer2_hits	primer2_snpsmaxfreq	primer2_snps	amplicon_fts	remarks
17	41226318	41226487	test	41226293	41226510	+	AGGATTCAGAGTAAAATCAAAGTGT	GATGATAGGTGGTACATGCACAG	1	17:41226318-41226487	26	7.000000000000001e-5rs869312522(snp@chr17:41226294-41226295;freq=0;valid=by-cluster;submitterCount=2) rs762883588(snp@chr17:41226315-41226316;freq=7.000000000000001e-5;valid=by-frequency;submitterCount=1) rs273900738(snp@chr17:41226316-41226317;freq=0;valid=unknown;submitterCount=1)	15	0.99997	rs1800744(snp@chr17:41226487-41226488;freq=0.99791;valid=by-cluster,by-frequency,by-1000genomes;submitterCount=16) rs397509183(del@chr17:41226487-41226489;freq=0;valid=unknown;submitterCount=1) rs80357137(snp@chr17:41226488-41226489;freq=0;valid=unknown;submitterCount=1) rs80357534(del@chr17:41226488-41226490;freq=0;valid=unknown;submitterCount=1) rs397509182(del@chr17:41226494-41226495;freq=0;val

wdecoster

name	primer1	primer2
test	AGGATTCAGAGTAAAATCAAAGTGT	GATGATAGGTGGTACATGCACAG

wdecoster

import pysam
import sys
import matplotlib.pyplot as plt
import numpy as np

def main(bam):
	samfile = pysam.AlignmentFile(bam)
	ratios = np.array([indelratio(read.cigartuples) for read in samfile.fetch()])
	n, bins, patches = plt.hist(ratios, bins=[i/10 for i in range(1,50, 1)])
	plt.xlabel('indel ratio')

wdecoster

import fdb

con = fdb.connect(dsn='molgenvz.cde.ua.ac.be:/home/firebird/gentli.fdb',
                  user='wdc',
                  password="mypassword",
                  role='NBD_SC')
cur = con.cursor()
cur.execute('select "id", "sample_individual", "sample_sample", "experiment_id", \
            "experiment_description", "wes_project" from "NBD_SC:full_wes" \
            where \