test_subset.sh - miRNA analysis - urllib.error.HTTPError: HTTP Error 404: Not Found

[kubu4]

It seems like the URL for downloading miRBase is different than what is utilized in the code. Current URL is:

https://www.mirbase.org/download/CURRENT/

However, XICRA/modules/database.py has this:

    ## miRBase ftp site
    ftp_site = "https://www.mirbase.org/ftp/CURRENT/"

As such, when running test_subset.sh, the following error gets thrown during miRNA analysis:

|==================================================|
|                  miRNA analysis                  |
|==================================================|


--------- Starting Process ---------
	03/29/2024, 09:30:06

+ Software for miRNA analysis selected:
['miraligner']
+ Getting files from input folder... 
+ Mode: join.
+ Extension: 
[_joined.fastq]

+ Input folder exists
	5 files selected...
	5 samples selected...
	Single end mode selected...
+ Species provided: hsa
+ Create folder to store results:  /home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/site-packages/XICRA/modules/db_files
+ File miRNA gff3 annotation
	** Download it form miRBase
Traceback (most recent call last):
  File "/home/sam/programs/mambaforge/envs/XICRA_env/bin/XICRA", line 398, in <module>
    args.func(args)
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/site-packages/XICRA/modules/miRNA.py", line 148, in run_miRNA
    options = database.miRNA_db(options)    
              ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/site-packages/XICRA/modules/database.py", line 101, in miRNA_db
    options.miRNA_gff = functions.main_functions.urllib_request(options.miRNA_db, ftp_site1, file_name, Debug)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/site-packages/HCGB/functions/main_functions.py", line 221, in urllib_request
    urllib.request.urlretrieve(url_string, file_path_name )
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/urllib/request.py", line 240, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
                            ^^^^^^^^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/urllib/request.py", line 215, in urlopen
    return opener.open(url, data, timeout)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/urllib/request.py", line 521, in open
    response = meth(req, response)
               ^^^^^^^^^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/urllib/request.py", line 630, in http_response
    response = self.parent.error(
               ^^^^^^^^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/urllib/request.py", line 559, in error
    return self._call_chain(*args)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/urllib/request.py", line 492, in _call_chain
    result = func(*args)
             ^^^^^^^^^^^
  File "/home/sam/programs/mambaforge/envs/XICRA_env/lib/python3.12/urllib/request.py", line 639, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found


Fri Mar 29 09:30:06 PDT 2024 ... Paired End Test finished ...

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