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from contextlib import contextmanager
import functools

import numpy as np

import gsd
import gsd.hoomd

import hoomd
import hoomd.md

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# from https://stackoverflow.com/questions/22712292/how-to-use-numpy-savez-in-a-loop-for-save-more-than-one-array/22716159#22716159

import numpy as np
import tempfile

class my_savez(object):
    def __init__(self, file, compression=None, compresslevel=None):
        # Import is postponed to here since zipfile depends on gzip, an optional
        # component of the so-called standard library.
        import zipfile

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import subprocess
import shutil
import argparse
import pathlib

parser = argparse.ArgumentParser(description='Download all SRAs from a GSM.')
parser.add_argument('GSMs', metavar='GSMs', type=str, nargs='+',
                   help='GSMs to download, can be more than one')
parser.add_argument('-g', '--guess-title',
                   help='If specified, guess the title of each GSMs and use it to store SRRs',

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#!/bin/sh
if ! type "efetch" > /dev/null; then
  print "Please install E-utilitie."
fi

GSM_LIST=$1
GSMs=`cat $GSM_LIST|cut -f1`
#echo $SRRs 
! type "foo" > /dev/null 2>&1;
for GSM in $GSMs; do

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