Commit 05ac5412 runtime bug

[ksahlin]

I am working on commit 05ac5412120c41cf764f858a9c53742dc1df9996 and it gives

$ python -m pyinstrument main.py --fastq ~/data/isONform_data/correction/1/corrected_reads_subset10.fastq --exact_instance_limit 50 --k 20 --w 31 --xmin 14 --xmax 80 --max_seqs_to_spoa 200 --delta_len 5 --outfolder ~/data/isONform_data/out_single --iso_abundance 2 --exact
xmin set to 40
Input:  /Users/ksahlin/data/isONform_data/correction/1/corrected_reads_subset10.fastq
False
Temporary workdirektory: /var/folders/37/bd97s8vs4pq9qp590z0tgm840000gn/T/tmp0zs_e860
Window used for batch: 31
Working on 10 reads in a batch
13649 MINIMIZER COMBINATIONS GENERATED
Average abundance for non-unique minimizer-combs: 5.807065217391305
Number of singleton minimizer combinations filtered out: 827
Working on all reads
Generating the graph
54  Nodes in our Graph
Traceback (most recent call last):
  File "/Users/ksahlin/opt/anaconda3/envs/isonform/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/Users/ksahlin/opt/anaconda3/envs/isonform/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/Users/ksahlin/opt/anaconda3/envs/isonform/lib/python3.6/site-packages/pyinstrument/__main__.py", line 292, in <module>
    main()
  File "/Users/ksahlin/opt/anaconda3/envs/isonform/lib/python3.6/site-packages/pyinstrument/__main__.py", line 163, in main
    exec_(code, globs, None)
  File "<string>", line 1, in <module>
  File "/Users/ksahlin/opt/anaconda3/envs/isonform/lib/python3.6/runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "/Users/ksahlin/opt/anaconda3/envs/isonform/lib/python3.6/runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "/Users/ksahlin/opt/anaconda3/envs/isonform/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "main.py", line 1029, in <module>
    main(args)
  File "main.py", line 861, in main
    is_cyclic=isCyclic(DG)
  File "/Users/ksahlin/prefix/source/isONform/SimplifyGraph.py", line 58, in isCyclic
    CNode = namedtuple('CNode', 'visited recStack',defaults=(False,False))
TypeError: namedtuple() got an unexpected keyword argument 'defaults'

[ksahlin]

Perhaps a python version issue? I am using python 3.6.11.

[ksahlin]

Fixed in by CNode = namedtuple('CNode', 'visited recStack') in line 58 in simplifyGraph.py. Probably version inconsistency or something.

[aljpetri]

That is very possible due to the namedtuple

Kristoffer @.***> schrieb am Fr., 25. Nov. 2022, 15:48:

Perhaps a python version issue? I am using python 3.6.11.

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