golobor

import h5py
import argparse

def copy_dataset(source_file, destination_file, source_dataset, destination_dataset, overwrite):
    with h5py.File(source_file, 'r') as source:
        with h5py.File(destination_file, 'a') as destination:
            if source_dataset not in source:
                print(f"Dataset '{source_dataset}' does not exist in the source file.")
                return
            

golobor

from contextlib import contextmanager
import functools

import numpy as np

import gsd
import gsd.hoomd

import hoomd
import hoomd.md

golobor

golobor

golobor

golobor

# 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

golobor

golobor

golobor

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',

golobor

#!/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