clintval

from cyvcf2 import VCFReader

from snv_spectrum import Snv

reader = VCFReader(str(root / 'all.ann.vcf'))
samples = reader.samples

for variant in reader:
    for sample, depth, alt_depth, gt_base in zip(
        samples,

clintval

from itertools import combinations, product

def hamming_circle(word, n, alphabet):
    """Create all words of hamming distance `n` in a given alphabet from a
    target word.

    Examples
    ---
    >>> sorted(hamming_circle('abc', 0, 'abc'))
    ['abc']

clintval

import numpy as np
import scipy.stats as stats

__all__ = [
    'gaussian_1d_mixture',
    'gaussian_2d_mixture']


def gaussian_1d_mixture(arr, cov_factor=0.2):
    """A Gaussian kernel density estimation with a tuneable covariance factor.

clintval

from typing import Any, Callable, Optional

class wait_callable_true(object):
    """Wait until a callable evaluates to a truthy statement, then continue.
    
    This object can be used as a function or as a context manager.

    Args:
        callable: A function which should eventually return a truthy value.
        call_rate: The rate at which to test the callable, optional.

clintval

$ffmpeg -i in.mov -pix_fmt rgb8 -r 10 output.gif && gifsicle -O3 output.gif -o output.gif

clintval

Note: Build 37 coordinates.

TCGA-AB-2812   13 28608256 28608257 -  TCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAG
TCGA-AB-2825   13 28608217 28608218 -  CCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTATTCGTG
TCGA-AB-2830   13 28608242 28608243 -  ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG
TCGA-AB-2836   13 28608267 28608268 -  TTCTCTGAAATCAACGTAGAAGTACTCATTATC
TCGA-AB-2840   13 28608248 28608249 -  ATTTGAGATCATATTCAT
TCGA-AB-2844   13 28608214 28608215 -  TTACCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCT
TCGA-AB-2853   13 28608268 28608269 -  TCTCTGAAATCAACGTAG

clintval

from types import MethodType


class TypeSafeAttribute(object):
    def _type_of(self, attr):
        if not self._has_attr(attr):
            raise ValueError(f'No attribute defined as annotation: {attr}')
        return self.__annotations__[attr]

    def _has_attr(self, attr):

clintval

clintval

  
  /** Implicit methods for [[Template]] objects. */
  implicit class TemplateUtil(val t: Template) {
    private def tagValue[A](records: Iterator[SamRecord], tag: String): Iterator[Option[A]] = records.map(_.get[A](tag))
    def bestEditDistanceToReference(t: Template): Option[Int]  = tagValue[Int](t.allReads, SAMTag.NM.name).min
    def worstEditDistanceToReference(t: Template): Option[Int] = tagValue[Int](t.allReads, SAMTag.NM.name).max
    def bestAlignmentScore(t: Template): Option[Int]           = tagValue[Int](t.allReads, SAMTag.AS.name).max
    def worstAlignmentScore(t: Template): Option[Int]          = tagValue[Int](t.allReads, SAMTag.AS.name).min
  }

clintval

package com.clintval.misc

trait CommandLineTool {
  val Executable: String
  def exec(args: String*): ProcessBuilder = { new ProcessBuilder(Executable +: args: _*) }
}

trait Testable {
  self: CommandLineTool =>
  val TestCommand: Seq[String]