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@golobor
golobor / h5cp.py
Created December 12, 2023 12:51
h5cp
View h5cp.py
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
View shared_hoomd_poly.py
from contextlib import contextmanager
import functools
import numpy as np
import gsd
import gsd.hoomd
import hoomd
import hoomd.md
@golobor
golobor / 230306-symmetrize-stack.ipynb
Last active March 6, 2023 20:32
230306-symmetrize-stack
View 230306-symmetrize-stack.ipynb
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@golobor
golobor / hela-pairing.ipynb
Created October 14, 2022 15:18
region-wide-P(s)
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@golobor
golobor / bottle-brush-scaling-theory.ipynb
Created June 22, 2020 20:26
Bottle Brush P(s) theory for Gibcus et at 2018
View bottle-brush-scaling-theory.ipynb
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View my_savez.py
# 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 / yeast_cohesin_project_fig6.ipynb
Created December 14, 2018 06:09
Yeast dCohesin Hi-C, fig6
View yeast_cohesin_project_fig6.ipynb
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@golobor
golobor / w303.centromeres.tsv
Last active December 14, 2018 05:50
Yeast cohesin supplemental files (w303 genome)
View w303.centromeres.tsv
chrom start end
chrVII 496916 497034
chrVI 148509 148626
chrV 151987 152104
chrIV 449712 449822
chrIII 114385 114501
chrII 238206 238322
chrI 151465 151582
chrIX 355629 355745
chrVIII 105591 105708
View sra_downloader.py
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
golobor / gist:fea8b74fce5e1b8119e6c8dc96671f07
Created December 1, 2018 05:52 — forked from suimye/gist:d8edec74cce9ecad86cd
For retrieving fastq file from NCBI GEO using GSM number.
View gist:fea8b74fce5e1b8119e6c8dc96671f07
#!/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