lozybean

colorfun=function(feature) {
    if(feature.get('cosmic_attrs')) return 'red';
    else if(feature.get('clinvar_attrs')) return 'cyan';
    else if(feature.get('dbsnp_attrs')) return 'green';
    else if(feature.get('snpeff_attrs')) return 'goldenrod';
    else if(feature.get('snpeff_0_attrs')) return 'orange';
    else if(feature.get('wellderly_attrs')) return 'purple';
    else return 'lightgreen';
  }

lozybean

class VariantRecord(object):
    def __init__(self, chrom, pos, ref, alt,
                 ref_genome=ref_genome):
        self.chrom = chrom
        self.pos = int(pos)
        self.ref = ref
        self.alt = alt
        if isinstance(ref_genome, RefGenome):
            self.ref_genome = ref_genome
        else:

lozybean

#!/bin/bash

REMOTE_DIR=
USER=
PASSWD=
HOST=ftp://

lftp -u ${USER},${PASSWD} ${HOST} << EOF
mirror --use-pget-n=10 ${REMOTE_DIR}
bye

lozybean

#!/usr/bin/env python
# -*- coding: utf-8 -*- \#
"""
@author = 'liangzb'
@date = '2016/10/28 0028'

This script is used for FILTER marker in .vcf files
1. if filterName or genotypeFilterName is startswith 'SNP'
or 'INDEL', only corresponding record will be check.
2. filterExpression and genotypeFilterExpression is a simple

lozybean

# execly.py
#
# Example of generating code and executing it with exec()
# in the context of descriptors/metaclasses

from inspect import Parameter, Signature
import re
import time
from collections import OrderedDict

lozybean

#!/usr/bin/env python
# -*- coding: utf-8 -*- \#
"""
@author = 'liangzb'
@date = '2016/7/13 0013'

This script is for official clinvar.vcf file's
normalization and satisficing ANNOVAR format.

samtools is needed for reference read.

lozybean

#!/usr/bin/env python
# -*- coding: utf-8 -*- \#
"""
@author = 'liangzb'
@date = '2016/7/5 0005'

"""

import abc