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

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

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

#!/usr/bin/env python

import os
import sys

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

import argparse

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

# Author: denis.engemann@gmail.com
# License: simplified BSD (3 clause)
# Note: code is based on scipy.stats.pearsonr

def ss(a, axis):
    return np.sum(a * a, axis=axis)

def compute_corr(x, y):
    x = np.asarray(x)
    y = np.asarray(y)

endrebak

# ctypedef struct ailist_t:
#     int64_t nr, mr  					# Number of regions
#     interval_t *interval_list			# Regions data
#     uint32_t first, last				# Record range of intervals
#     int nc, lenC[10], idxC[10]
#     uint32_t *maxE
# ...
#     uint32_t binary_search(interval_t* As, uint32_t idxS, uint32_t idxE, uint32_t qe) nogil

endrebak

# wget http://big.databio.org/example_data/AIList/AIListTestData.tgz

nrows = 1.5e6

from ncls import NCLS
from ailist import AIList

import numpy as np
import pandas as pd

endrebak

# Works on very large datasets.

import pandas as pd

try:
    import mkl
    mkl.set_num_threads(1)
except:
    pass

endrebak

{
    "global": {
        "check_for_updates_on_startup": true,
        "show_in_menu_bar": true,
        "show_profile_name_in_menu_bar": false
    },
    "profiles": [
        {