odinokov

"""
VCF.py
Kamil Slowikowski
October 30, 2013

Read VCF files. Works with gzip compressed files and pandas.

Note: This module ignores the genotype columns because
      I didn't need them at the time of writing.

odinokov

#!/usr/bin/env python

import io
import os
import pandas as pd


def read_vcf(path):
    with open(path, 'r') as f:
        lines = [l for l in f if not l.startswith('##')]

odinokov

'''
Sorting Pandas dataframe by frequency of occurrence in one column
'''
df_ = df.copy()
df_['count'] = df_.groupby('myTAG')['myTAG'].transform('count')
df_ = df_.sort_values(by=['count']).drop(['count'], axis=1).reset_index(drop=True)
df = df_

odinokov

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (C) 2016 by Gaik Tamazian
# mail (at) gtamazian (dot) com

import argparse
import glob
import logging
import os

odinokov

#GATK Method <- Slower and keeps original ID plut dbSNP rsID
# R=Reference FASTA
# V=VCF file to add IDs to
# --dbsnp = dbsnp VCF -- download from NCBI FTP

java -jar GenomeAnalysisTK.jar -R /reference/Homo_sapiens_assembly19.fasta -T VariantAnnotator -V vcf_to_add_id_to.vcf --dbsnp /reference/dbsnp_137.b37.vcf.gz --out /data/Broad.chr1.annotated.vcf

#bcftools Method <- Faster, replaces existing ID with dbSNP rsID
/usr/bin/htslib/bcftools/bcftools annotate -a /reference/dbsnp_137.b37.vcf.gz -c ID vcf_to_add_id_to.vcf

odinokov

#  Copyright (c) 2013 Alexandre Drouin. All rights reserved.
#
#  Permission is hereby granted, free of charge, to any person obtaining a copy of
#  this software and associated documentation files (the "Software"), to deal in
#  the Software without restriction, including without limitation the rights to
#  use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
#  of the Software, and to permit persons to whom the Software is furnished to do
#  so, subject to the following conditions:
#
#  The above copyright notice and this permission notice shall be included in all

odinokov

from entropy import * # https://raphaelvallat.com/entropy/build/html/index.html
import hfda # https://pypi.org/project/hfda/ Higuchi Fractal Dimension Analysis
import numpy as np

L1 = '000000000011111111110' # less patterns
L2 = '010101010101010101011' # more patterns

def seq2list(l):
    return np.array(list(map(int, list(l))))

odinokov

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Sliding windows module.
"""

import numpy as np

from numpy.lib.stride_tricks import as_strided

odinokov

I have reused the code enough to make a package out of it.

The python package is deposited at Github. with an example in Jupyter notebook.

odinokov

import numpy

def mode(ndarray, axis=0):
    
    '''
    from https://stackoverflow.com/questions/16330831/most-efficient-way-to-find-mode-in-numpy-array
    '''
    # Check inputs
    ndarray = numpy.asarray(ndarray)
    ndim = ndarray.ndim