clintval

import textwrap

from operator import itemgetter
from Bio.Seq import reverse_complement
from pyfaidx import Fasta, FetchError
from collections import Counter, defaultdict, OrderedDict

from pymutagenesis.seq import *

link = '<a target="_blank" href={}>{}</a>'

clintval

{
  "A10": [
    0.0034329041, 0.0137316166, 0.0344053282, 0.0188924926, 0.0240140593,
    0.0212451426, 0.0821539635, 0.0064712216, 0.0620039955, 0.0524827040,
    0.2530320358, 0.0485341620, 0.0114430138, 0.0159038497, 0.0332954789,
    0.0099940168, 0.0068658083, 0.0000000000, 0.0062555142, 0.0113354956,
    0.0026682288, 0.0070817142, 0.0072488791, 0.0161780540, 0.0074404795,
    0.0071567324, 0.0295204042, 0.0000000000, 0.0022886028, 0.0000000000,
    0.0030268617, 0.0099940168, 0.0000000000, 0.0000000000, 0.0218942998,
    0.0000000000, 0.0000000000, 0.0035408571, 0.0144977583, 0.0032356108,

clintval

#!/bin.sh
# request Bourne shell as shell for job
#$ -S /bin/sh
#$ -cwd
#$ -V
#$ -m e
#$ -pe whole_nodes 7
#$ -M valentine.clint@gmail.com
###############################
module add bwa/0.6.1

clintval

class IgvCanvasToStatic(object):
    def __init__(self):
        self._javascript = """
        // Converts canvas to an image
        function convertCanvasToImage(canvas)
        {
            var image = canvas.toDataURL("image/png");
            return '<img src="' + image + '"/>';
        }

clintval

import contextlib
import sys

import pandas as pd

try:
    import pandas.io.formats.format as pf
except ImportError:
    import pandas.formats.format as pf
except ImportError:

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import base64

import matplotlib.pyplot as plt

from matplotlib import animation
from tempfile import NamedTemporaryFile

__all__ = [
    'Animation',
    'animate_3d_scatter']

clintval

rule illumina_basecalls_to_sam:
    input:
        basecalls_dir=basecalls_dir,
        barcodes_dir=rules.extract_illumina_barcodes.output.barcodes_dir,
        library_params=rules.create_basecalling_params.output.library_params
    output: list_unmerged_sample_bam()
    threads: max(1, int(threads / len(lanes)))
    resources:
        gc_time_limit=50,
        gc_heap_free_limit=10,

clintval

# Maintainer: Clint Valentine <valentine.clint@gmail.com>

pkgname=vep
pkgver=90.10
pkgrel=1
pkgdesc="Determines the effect of variants on genes, transcripts, and protein sequences as well as regulatory regions"
arch=('x86_64')
url="https://useast.ensembl.org/info/docs/tools/vep/index.html"
license=('GPL3')
depends=('perl>=5' 'perl-module-build' 'bioperl-live-git')

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# Maintainer: Clint Valentine <valentine.clint@gmail.com>

pkgname=polyphen
pkgver=2.2.2r405c
pkgrel=1
dbver=2.2.2
blastver=2.7.1
pkgdesc="A tool to predict impact of amino acid substitutions on the structure and function of human proteins"
arch=('any')
url="http://genetics.bwh.harvard.edu/pph2/dokuwiki/downloads"

clintval