Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

AttributeError: 'NoneType' object has no attribute 'group' #96

Open
yye88 opened this issue May 18, 2023 · 4 comments
Open

AttributeError: 'NoneType' object has no attribute 'group' #96

yye88 opened this issue May 18, 2023 · 4 comments

Comments

@yye88
Copy link

yye88 commented May 18, 2023

Hello, dear author, recently I was doing a regular cblaster search, but I encountered the following error during the running process.
[16:18:05] INFO - Search has completed successfully!
[16:18:05] INFO - Retrieving results for search 6BPHW1VJ016
Traceback (most recent call last):
File "/home/yye/miniconda3/bin/cblaster", line 8, in
sys.exit(main())
File "/home/yye/miniconda3/lib/python3.9/site-packages/cblaster/main.py", line 432, in main
cblaster(
File "/home/yye/miniconda3/lib/python3.9/site-packages/cblaster/main.py", line 318, in cblaster
rid, results = remote.search(
File "/home/yye/miniconda3/lib/python3.9/site-packages/cblaster/remote.py", line 371, in search
results = retrieve(rid, hitlist_size=hitlist_size)
File "/home/yye/miniconda3/lib/python3.9/site-packages/cblaster/remote.py", line 208, in retrieve
for line in re.search("

(.+?)
", response.text, re.DOTALL)
AttributeError: 'NoneType' object has no attribute 'group'

Could you guide me on how to solve it? Thank you very much.
@kcamnairb
Copy link

kcamnairb commented Apr 2, 2024 •
edited
Loading

I'm also encountering this same problem.

[11:10:46] INFO - Retrieving results for search 0SB0MXJK013
Traceback (most recent call last):
  File "/home/brian/anaconda3/envs/clinker_env/bin/cblaster", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/brian/anaconda3/envs/clinker_env/lib/python3.11/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/home/brian/anaconda3/envs/clinker_env/lib/python3.11/site-packages/cblaster/main.py", line 318, in cblaster
    rid, results = remote.search(
                   ^^^^^^^^^^^^^^
  File "/home/brian/anaconda3/envs/clinker_env/lib/python3.11/site-packages/cblaster/remote.py", line 371, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/brian/anaconda3/envs/clinker_env/lib/python3.11/site-packages/cblaster/remote.py", line 209, in retrieve
    .group(1)
     ^^^^^
AttributeError: 'NoneType' object has no attribute 'group'

@steffk1
Copy link

steffk1 commented May 13, 2024

Hej!
I'm still running into this issue in version 1.3.18 running cblast search.

from the log:

[10:56:00] INFO - Checking search status...
[10:56:00] INFO - Search has completed successfully!
[10:56:00] INFO - Retrieving results for search 44BBGM0G013
Traceback (most recent call last):
  File "/home/steffk1/.conda/envs/cblaster/bin/cblaster", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/steffk1/.conda/envs/cblaster/lib/python3.12/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/home/steffk1/.conda/envs/cblaster/lib/python3.12/site-packages/cblaster/main.py", line 318, in cblaster
    rid, results = remote.search(
                   ^^^^^^^^^^^^^^
  File "/home/steffk1/.conda/envs/cblaster/lib/python3.12/site-packages/cblaster/remote.py", line 371, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/steffk1/.conda/envs/cblaster/lib/python3.12/site-packages/cblaster/remote.py", line 209, in retrieve
    .group(1)
     ^^^^^
AttributeError: 'NoneType' object has no attribute 'group'

$ cblaster --version
Importing genomicsqlite failed, falling back to SQLite3
cblaster 1.3.18

And I would like to add one more quirk to the issue: I ran it erroneously first with one more gene in the BGC and didn't encounter this issue. Once I removed the gene and re-ran, this issue appeared.
Cheers,
Karin

@ystone1101
Copy link

ystone1101 commented May 31, 2024 •
edited
Loading

I'm also encountering this same problem.

[22:49:11] INFO - Starting cblaster in remote mode
[22:49:11] INFO - Launching new search
[22:49:13] INFO - Request Identifier (RID): 5KNASY6N013
[22:49:13] INFO - Request Time Of Execution (RTOE): 28s
[22:49:41] INFO - Polling NCBI for completion status
[22:49:41] INFO - Checking search status...
[22:50:41] INFO - Checking search status...
[22:51:41] INFO - Checking search status...
[22:52:41] INFO - Checking search status...
[22:53:41] INFO - Checking search status...
[22:54:41] INFO - Checking search status...
[22:55:41] INFO - Checking search status...
[22:56:41] INFO - Checking search status...
[22:57:41] INFO - Checking search status...
[22:58:41] INFO - Checking search status...
[22:59:41] INFO - Checking search status...
[23:00:41] INFO - Checking search status...
[23:01:41] INFO - Checking search status...
[23:02:41] INFO - Checking search status...
[23:03:41] INFO - Checking search status...
[23:04:41] INFO - Checking search status...
[23:05:41] INFO - Checking search status...
[23:06:41] INFO - Checking search status...
[23:07:41] INFO - Checking search status...
[23:08:41] INFO - Checking search status...
[23:09:41] INFO - Checking search status...
[23:10:41] INFO - Checking search status...
[23:10:42] INFO - Search has completed successfully!
[23:10:42] INFO - Retrieving results for search 5KNASY6N013
Traceback (most recent call last):
File "/home/kys/anaconda3/envs/cblaster/bin/cblaster", line 8, in
sys.exit(main())
^^^^^^
File "/home/kys/anaconda3/envs/cblaster/lib/python3.12/site-packages/cblaster/main.py", line 432, in main
cblaster(
File "/home/kys/anaconda3/envs/cblaster/lib/python3.12/site-packages/cblaster/main.py", line 318, in cblaster
rid, results = remote.search(
^^^^^^^^^^^^^^
File "/home/kys/anaconda3/envs/cblaster/lib/python3.12/site-packages/cblaster/remote.py", line 371, in search
results = retrieve(rid, hitlist_size=hitlist_size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kys/anaconda3/envs/cblaster/lib/python3.12/site-packages/cblaster/remote.py", line 209, in retrieve
.group(1)
^^^^^
AttributeError: 'NoneType' object has no attribute 'group'

@Tim-Kirkwood
Copy link

Hello, me too :( Trace is at the bottom, I think the issues lies with the html parsing after you query NCBI for the RID:

def retrieve(rid, hitlist_size=5000):
    """Retrieve BLAST results corresponding to a given Request Identifier (RID).

    Arguments:
        rid (str): NCBI BLAST search request identifiers (RID)
        hitlist_size (int): Total number of hits to retrieve
    Returns:
        list: BLAST search results split by newline, with HTML parts removed
    """

    parameters = {
        "CMD": "Get",
        "RID": rid,
        "FORMAT_TYPE": "Tabular",
        "FORMAT_OBJECT": "Alignment",
        "HITLIST_SIZE": hitlist_size,
        "ALIGNMENTS": hitlist_size,
        "DESCRIPTIONS": hitlist_size,
        "NCBI_GI": "F",
    }

    LOG.debug(parameters)

    response = requests.get(BLAST_API_URL, params=parameters)

    LOG.debug(response.url)

    # Remove HTML junk and info lines
    # BLAST results are stored inside <PRE></PRE> tags
    return [
        line
        for line in re.search("<PRE>(.+?)</PRE>", response.text, re.DOTALL)
        .group(1) #####This line############
        .split("\n")
        if line and not line.startswith("#")
    ]

Traceback:

(pip_env) C:\Users\my_username>cblaster search -qf "fasta\path.fasta" -mh 11 -b "binary\path.txt" -bde ","
Importing genomicsqlite failed, falling back to SQLite3
[14:15:44] INFO - Starting cblaster in remote mode
[14:15:44] INFO - Launching new search
[14:15:46] INFO - Request Identifier (RID): 78AW18TZ016
[14:15:46] INFO - Request Time Of Execution (RTOE): 10s
[14:15:56] INFO - Polling NCBI for completion status
[14:15:56] INFO - Checking search status...
[14:16:56] INFO - Checking search status...
[14:17:56] INFO - Checking search status...
[14:18:56] INFO - Checking search status...
[14:19:56] INFO - Checking search status...
[14:20:56] INFO - Checking search status...
[14:21:56] INFO - Checking search status...
[14:22:56] INFO - Checking search status...
[14:23:56] INFO - Checking search status...
[14:24:56] INFO - Checking search status...
[14:25:56] INFO - Checking search status...
[14:26:56] INFO - Checking search status...
[14:27:56] INFO - Checking search status...
[14:28:56] INFO - Checking search status...
[14:29:56] INFO - Checking search status...
[14:30:56] INFO - Checking search status...
[14:31:56] INFO - Checking search status...
[14:32:56] INFO - Checking search status...
[14:33:56] INFO - Checking search status...
[14:34:56] INFO - Checking search status...
[14:35:56] INFO - Checking search status...
[14:36:56] INFO - Checking search status...
[14:37:56] INFO - Checking search status...
[14:38:56] INFO - Checking search status...
[14:39:56] INFO - Checking search status...
[14:40:56] INFO - Checking search status...
[14:40:56] INFO - Search has completed successfully!
[14:40:56] INFO - Retrieving results for search 78AW18TZ016
Traceback (most recent call last):
  File "C:\Users\u03132tk\AppData\Local\anaconda3\envs\pip_env\lib\runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\u03132tk\AppData\Local\anaconda3\envs\pip_env\lib\runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "C:\Users\u03132tk\AppData\Local\anaconda3\envs\pip_env\Scripts\cblaster.exe\__main__.py", line 7, in <module>
  File "C:\Users\u03132tk\AppData\Local\anaconda3\envs\pip_env\lib\site-packages\cblaster\main.py", line 432, in main
    cblaster(
  File "C:\Users\u03132tk\AppData\Local\anaconda3\envs\pip_env\lib\site-packages\cblaster\main.py", line 318, in cblaster
    rid, results = remote.search(
  File "C:\Users\u03132tk\AppData\Local\anaconda3\envs\pip_env\lib\site-packages\cblaster\remote.py", line 371, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
  File "C:\Users\u03132tk\AppData\Local\anaconda3\envs\pip_env\lib\site-packages\cblaster\remote.py", line 209, in retrieve
    .group(1)
AttributeError: 'NoneType' object has no attribute 'group'

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
5 participants
@kcamnairb @Tim-Kirkwood @yye88 @ystone1101 @steffk1