suqingdong

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Filename: merge_snp.py
# Date: 2016-09-23
# Author: suqingdong


class MergeSNP:
    '''
    Merge all the samples according to the second column(pos),

suqingdong

#!/usr/bin/env python
#======================
# Date: 2016-10-10
# Author: suqingdong
# Introductions: get gene list from annovar annotation result file, then generate a bed file from origin bed.
# Usage: python getGeneBed.py <genelist> <originbed> [outbed]
#======================
import re

suqingdong

#!/usr/bin/env python
# Extract columns: 'ChROM POS ID REF ALT GeneName' + samples' columns

def safe_open(infile):    
    try:
        if infile.endswith('.gz'):
            import gzip
            return gzip.open(infile)
        else:
            return open(infile)

suqingdong

#!/usr/bin/env python

import re

# One gene may exist in different chromsomes
# One position may belong diffrent genes
# geneList format:
# {'genename1': {
#    "chr1": [(start1,stop1), (start2, stop2)],
#    "chr2": [(start1,stop1), (start2, stop2)]

suqingdong

#!/usr/bin/env python
#=======================================================
# convert pos and samples
# row name is sample name, and column name is position
# value is the number of alt (0,1,2)
#=======================================================

# sampledict: {'sample1':['0','2',...], ...}
def convertSNP(infile, outfile):
    with open(infile) as f:

suqingdong

#!/usr/bin/env python
#======================================
# merge file1 and file2 of replaced.xls
# if no pos, mark '0'
# output coverted.xls
#======================================

# sampledict structure: {'sample1': {'pos1':'snp1','pos2':'snp2',... }, ...}
def getSampleDict(infile):
    sampledict = {}

suqingdong

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

def get_sample_list(infofile, listfile):
    sampledict = {}
    with open(infofile) as f:
        for line in f:
            sampleid,novoid = line.strip().split('\t')[2:4]
            sampledict[novoid] = sampleid
    

suqingdong

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

 
def get_sample_info(infofile, pn, disease):
    header = '#B1\n#FamilyID\tSampleID\tSex\tNormal/Patient\tPN'
    if disease:
        header += '\tDisease'
    header += '\n'

suqingdong

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

import sys


def add_count_samples(infile, outfile=None):
    outfile = outfile or infile+'.addCountSamples'
    with open(infile) as f, open(outfile, 'w') as out:
        for line in f:

suqingdong

#!/usr/bin/env python
# A simple example of crawler with requests and BeautifulSoup
# Pay attention to encoding

import bs4
import requests


def main(genelist):
    with open(genelist) as f: