Chromsizes URL

[SteveTur]

Hi, I tried to run:

Get chromosome sizes (for hg38 here)

import pyranges as pr import requests import pandas as pd target_url='http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes' chromsizes=pd.read_csv(target_url, sep='\t', header=None) chromsizes.columns=['Chromosome', 'End'] chromsizes['Start']=[0]*chromsizes.shape[0] chromsizes=chromsizes.loc[:,['Chromosome', 'Start', 'End']]

Exceptionally in this case, to agree with CellRangerARC annotations

chromsizes['Chromosome'] = [chromsizes['Chromosome'][x].replace('v', '.') for x in range(len(chromsizes['Chromosome']))] chromsizes['Chromosome'] = [chromsizes['Chromosome'][x].split('')[1] if len(chromsizes['Chromosome'][x].split('')) > 1 else chromsizes['Chromosome'][x] for x in range(len(chromsizes['Chromosome']))] chromsizes=pr.PyRanges(chromsizes)

I did it for several samples before and it was working well. However, now it seems like the link is not working anymore and i got the following error:

HTTPError Traceback (most recent call last) /Users/stur/Teaseq/Scenicplus/BM4/Scenicplus_BM4_Part_1.ipynb Cell 42 line 6 4 import pandas as pd 5 target_url='http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes' ----> 6 chromsizes=pd.read_csv(target_url, sep='\t', header=None) 7 chromsizes.columns=['Chromosome', 'End'] 8 chromsizes['Start']=[0]*chromsizes.shape[0]

File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/pandas/util/_decorators.py:211, in deprecate_kwarg.._deprecate_kwarg..wrapper(*args, *kwargs) 209 else: 210 kwargs[new_arg_name] = new_arg_value --> 211 return func(args, **kwargs)

File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/pandas/util/_decorators.py:317, in deprecate_nonkeyword_arguments..decorate..wrapper(*args, *kwargs) 311 if len(args) > num_allow_args: 312 warnings.warn( 313 msg.format(arguments=arguments), 314 FutureWarning, 315 stacklevel=find_stack_level(inspect.currentframe()), 316 ) --> 317 return func(args, **kwargs)

File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/pandas/io/parsers/readers.py:950, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, error_bad_lines, warn_bad_lines, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options) 935 kwds_defaults = _refine_defaults_read( ... File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/urllib/request.py:643, in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg, hdrs) 642 def http_error_default(self, req, fp, code, msg, hdrs): --> 643 raise HTTPError(req.full_url, code, msg, hdrs, fp)

HTTPError: HTTP Error 403: Forbidden

I tried to copye the URL on a web browser and it is not working.

What should I do?

Best,

Steven

[wgao688]

For some reason UCSC changed access privileges. You need to use this link instead now: https://hgdownload-test.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes

[SteveTur]

Thank you! I have another problem in the next following step:

from scenicplus.wrappers.run_scenicplus import run_scenicplus try: run_scenicplus( scplus_obj = scplus_obj, variable = ['GEX_celltype'], species = 'hsapiens', assembly = 'hg38', tf_file = '/Users/stur/utoronto_human_tfs_v_1.01.txt', save_path = os.path.join(work_dir, 'scenicplus'), biomart_host = biomart_host, upstream = [1000, 150000], downstream = [1000, 150000], calculate_TF_eGRN_correlation = True, calculate_DEGs_DARs = True, export_to_loom_file = True, export_to_UCSC_file = True, path_bedToBigBed = '/Users/stur/BM4/', n_cpu = 12, _temp_dir = '/tmp/ray_spill') except Exception as e:

in case of failure, still save the object

dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=-1)
raise(e)

One of my other samples didn't encounter any issues with that step.

Here is the error:

I found similar errors on GitHub, but no solutions.

Thank you again for your help!

Best,

Steven

[SeppeDeWinter]

Hi @SteveTur

How does your motif enrichment look like? Are your motifs correctly annotated to TFs? Can you share an example motif enrichment output html file?

All the best,

Seppe

[ghuls]

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes seems accessible again.