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import argparse | |
import numpy as np | |
from chainer import Variable, FunctionSet, optimizers, cuda | |
import chainer.functions as F | |
import cv2 | |
import random | |
import cPickle as pickle | |
import sys | |
class ConvolutionalAutoencoder(FunctionSet): |
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install.packages("rzmq") | |
Installing package into ‘/home/dima/R/x86_64-pc-linux-gnu-library/3.2’ | |
(as ‘lib’ is unspecified) | |
--- Please select a CRAN mirror for use in this session --- | |
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rzmq_0.7.7.tar.gz' | |
Content type 'application/x-gzip' length 16246 bytes (15 KB) | |
================================================== | |
downloaded 15 KB | |
* installing *source* package ‘rzmq’ ... |
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python3 setup.py build_ext | |
setup.py build_ext | |
/netapp/home/dlituiev/.usr/py3/lib/ | |
Partial import of sklearn during the build process. | |
Generating cython files | |
Cythonizing sources | |
sklearn | |
Processing sklearn/_isotonic.pyx | |
Traceback (most recent call last): | |
File "/usr/bin/cython", line 7, in <module> |
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<Test-sra> | |
<Ngs> | |
<Latest> | |
<ncbi-vdb version=""/> | |
<ngs-sdk version=""/> | |
</Latest> | |
<LibManager.properties/> | |
<ncbi-vdb> | |
</ncbi-vdb> | |
<ngs-sdk> |
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from __future__ import division, print_function | |
import numpy as np | |
import pandas as pd | |
from pysnptools.snpreader import SnpData | |
from pysnptools.kernelreader import KernelData | |
from fastlmm.inference.lmm import LMM | |
def snp_from_pandas(df, pos = None): | |
indiv_ids = zip(df.index.tolist(), ["."] * len(df.index)) | |
snp_ids = [("_".join(["%s"% y for y in x]) if type(x) in (tuple, list) else "%s"% x) for x in df.columns.tolist()] |
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dfstr = '''{"FDR":{"0":0.0000001434,"1":0.0974543339,"2":0.5637882089,"3":0.7592318769,"4":0.82376489,"5":0.876232133,"6":0.891150062,"7":0.9234070548,"8":0.9421697501,"9":0.9421697501,"10":0.9534575004,"11":0.9686912495,"12":0.9792339965,"13":0.9800272087,"14":0.9814635178,"15":0.9814635178,"16":0.9822809925,"17":0.9832209543,"18":0.9832209543,"19":0.9832209543,"20":0.0079716299,"21":0.6863477759,"22":0.7846481266,"23":0.8596431336,"24":0.8940558933,"25":0.9071788194,"26":0.9269123036,"27":0.9323909829,"28":0.936505473,"29":0.9477474057,"30":0.9479119432,"31":0.9479119432,"32":0.9479119432,"33":0.9479119432,"34":0.9479179113,"35":0.9577011312,"36":0.9589141116,"37":0.9601000647,"38":0.9614078093,"39":0.9657393252,"40":0.0000000308,"41":0.1179302537,"42":0.6074557222,"43":0.7534315164,"44":0.8290719564,"45":0.8917851883,"46":0.9325332126,"47":0.9495263504,"48":0.9532127733,"49":0.9552555496,"50":0.9594234241,"51":0.9675706204,"52":0.9737916651,"53":0.9767958687,"54":0.9767958687,"55":0.9767958687,"56":0.97679 |
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import pandas as pd | |
all_cols = ['0_AnatomicRegionSequence_CodeMeaning', | |
'0_AnatomicRegionSequence_CodeValue', | |
'0_AnatomicRegionSequence_CodingSchemeDesignator', | |
'0_ContributingEquipmentSequence_ContributionDateTime', | |
'0_ContributingEquipmentSequence_ContributionDescription', | |
'0_ContributingEquipmentSequence_InstitutionName', | |
'0_ContributingEquipmentSequence_Manufacturer', | |
'0_ContributingEquipmentSequence_StationName', | |
'0_ContributingEquipmentSequence__0_PurposeOfReferenceCodeSequence_CodeMeaning', |
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import sys | |
import numpy as np | |
import keras | |
from keras.models import load_model, Model | |
from keras.layers import Conv2D, MaxPool2D, GlobalAveragePooling2D, Dense, Dropout | |
from keras import backend as K | |
from keras.applications.inception_v3 import InceptionV3 | |
def get_model( | |
dropout=0.5, |
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""" | |
Created on Wed Oct 25 13:44:51 2017 | |
@author: dlituiev | |
""" | |
import numpy as np | |
import keras | |
from keras import backend as K | |
from keras.layers import (InputLayer, Conv2D, Dense, Activation, | |
AveragePooling2D, GlobalAveragePooling2D) |
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#!/usr/bin/env python3 | |
# -*- coding: utf-8 -*- | |
""" | |
Created on Wed Oct 25 13:44:51 2017 | |
@author: dlituiev | |
""" | |
import os | |
import numpy as np | |
from uuid import uuid1 |
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