wdecoster

#! /usr/bin/env python
import os
import sys

def main():
    versionfile = [os.path.join(root, x) for root, dirs, files in os.walk(os.getcwd()) for x in files if x == "version.py"]
    if len(versionfile) == 1:
        with open(versionfile[0]) as versionf:
            version = versionf.read().split("\"")[1]
        os.system("git commit -m 'bumping version to {}' {}".format(version, versionfile[0]))

wdecoster

import pypandoc
long_description=pypandoc.convert(path.join(here, 'README.md'), 'rst'),

wdecoster

# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
import pypandoc

here = path.abspath(path.dirname(__file__))
exec(open('nanoplot/version.py').read())

wdecoster

from nanomath import aveQual
from nanoplotter import scatter
from Bio import SeqIO
import numpy as np
import pandas as pd
import sys
import gzip
from scipy import stats
import csv

wdecoster

from nanoplotter import scatter
import pandas as pd
import numpy as np
import sys
from scipy import stats
import pysam
from multiprocessing import Pool

def main():
    df = processBam(sys.argv[1], 24)

wdecoster

def aveQual(quals):
    '''
    Receive the integer quality scores of a read and return the average quality for that read
    First convert Phred scores to probabilities, calculate average error probability and convert average back to Phred scale
    '''
    return -10*math.log(sum([10**(q/-10) for q in quals]) / len(quals), 10)

wdecoster

def aveQual(quals):
    ''' 
    Receive the integer quality scores of a read and return the average quality for that read
    '''
    return sum(quals) / len(quals)

wdecoster

from nanomath import aveQual
from nanoplotter import scatter
from Bio import SeqIO
import pandas as pd
import numpy as np
import seaborn as sns
import sys
import gzip
import matplotlib.pyplot as plt
from scipy import stats

wdecoster

def makeLayout():
	'''
	Make the layout of the MinION flowcell, based on https://bioinformatics.stackexchange.com/a/749/681
	'''
	layoutlist = []
	for i, j in zip([33, 481, 417, 353, 289, 225, 161, 97], [8, 456, 392, 328, 264, 200, 136, 72]):
		for n in range(4):
			layoutlist.append(list(range(i+n*8, (i+n*8)+8, 1)) + list(range(j+n*8, (j+n*8)-8, -1)))
	return np.array(layoutlist)

wdecoster

# wdecoster

import os
import seaborn as sns
import numpy as np
import matplotlib.pyplot as plt
import argparse
import gzip
from Bio import SeqIO