endrebak

#!/usr/bin/env python2.7

### On SNPsnap
#!/bin/env python
#source /opt/rh/python27/enable
	#---> gives Python 2.7.5 (where as Broad Dotkit python is Python 2.7.1)

import os
import sys
import collections

endrebak

#!/usr/bin/env python

import os
import sys

import pandas as pd
import numpy as np
import pyranges as pr

import argparse

endrebak

def table(region, gwas_minus_region, total_gwas):

    pos_cols = "Chromosome Start End".split()
    total_region = len(region.drop_duplicates(pos_cols))

    tp = region.groupby("Trait").size()
    fp = (tp - total_region).abs()

    fn = gwas_minus_region.groupby("Trait").size()
    tn = ((fn + tp + fp) - total_gwas).abs()

endrebak

from scipy.stats import gaussian_kde
import numpy as np
import pandas as pd

df = pd.read_table(f, sep="\t")

values = df.CorrelationSum.sort_values()

gk = gaussian_kde(values)

endrebak

➜ head ~/Downloads/CEU/CEU-22-final.txt
Position(bp)	Rate(cM/Mb)	Map(cM)	Filtered
 16489239	0.0	0.0	1
 16494187	0.0	0.0	1
 16504399	0.0	0.0	1
 16855618	0.0	0.0	1
 16869887	0.0	0.0	1
 16872459	0.0	0.0	1
 16890307	0.0	0.0	1
 16923693	0.0	0.0	1

endrebak

index1 = 0
index2 = 0
while index1 < len(posin):
    pos = posin[index1]
    rs = rsin[index1]
    if pos == mappos[index2]:
        #the 1000 Genomes site was genotyped as part of the map
        results.append((rs, pos, mapgpos[index2]))
        index1 = index1 + 1

endrebak

#!/usr/bin/env python3

import sys, os, gzip, math
import numpy as np

# calculate Wen/Stephens shrinkage LD estimate
gmapfile = gzip.open(sys.argv[1]) # genetic map 
indfile = open(sys.argv[2]) #list of individuals
# NE = 11418.0
NE = float(sys.argv[3])

endrebak

def calc_diag_lean(self, out_fname, out_delim, dynamic_delete=True):

    if dynamic_delete == False:
        raise Exception('Error: Conversion has been run in lean mode, but with dynamically=False.')

    self.dynamic_delete = dynamic_delete

    flat.print_log_msg('Start')

endrebak

#!/usr/bin/env python3

import ldetect.baselib.flat_file_consts as cnst
import ldetect.baselib.flat_file as flat
import ldetect.baselib.binary_search as binsrch

import sys
import os.path
import math
import bisect

endrebak

# from . import flat_file_consts as cnst

import sys
import csv
import gzip
import time
import math
import bisect

def get_final_partitions(input_config, name, snp_first, snp_last):