GenoFLU 1.05 cannot analyze fasta files not in working directory

[peterk87]

GenoFLU installed from Bioconda

$ genoflu.py -f test/test-genome-A1.fasta

genoflu.py set arguements:

        FASTA:  test/test-genome-A1.fasta
        FASTA_dir:  None
        cross_reference:  None
        sample_name:  None
        debug:  False


Traceback (most recent call last):
  File "/home/pkruczkiewicz/miniforge3/envs/genoflu/bin/genoflu.py", line 372, in <module>
    genoflu = GenoFLU(FASTA=FASTA_abs_path, FASTA_dir=FASTA_dir,
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pkruczkiewicz/miniforge3/envs/genoflu/bin/genoflu.py", line 146, in __init__
    with open(FASTA_name, 'r') as f:
         ^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'test-genome-A1.fasta'

It looks like FASTA_name should be self.FASTA_abs_path

[stuber]

Try with your current working directory set as the “test” directory, so your working direct has the “test-genome-A1.fasta” file. Then run: `genoflu.py -f test-genome-A1.fasta` From: Peter Kruczkiewicz ***@***.***> Date: Thursday, January 16, 2025 at 11:03 AM To: USDA-VS/GenoFLU ***@***.***> Cc: Subscribed ***@***.***> Subject: [USDA-VS/GenoFLU] GenoFLU 1.05 cannot analyze fasta files not in working directory (Issue #12) GenoFLU installed from Bioconda $ genoflu.py -f test/test-genome-A1.fasta genoflu.py set arguements: FASTA: test/test-genome-A1.fasta FASTA_dir: None cross_reference: None sample_name: None debug: False Traceback (most recent call last): File "/home/pkruczkiewicz/miniforge3/envs/genoflu/bin/genoflu.py", line 372, in <module> genoflu = GenoFLU(FASTA=FASTA_abs_path, FASTA_dir=FASTA_dir, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkruczkiewicz/miniforge3/envs/genoflu/bin/genoflu.py", line 146, in __init__ with open(FASTA_name, 'r') as f: ^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'test-genome-A1.fasta' It looks like FASTA_name should be self.FASTA_abs_path — Reply to this email directly, view it on GitHub<#12>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABMMFMP4YMSHN47I62U6X632K7X5PAVCNFSM6AAAAABVKGMWVKVHI2DSMVQWIX3LMV43ASLTON2WKOZSG44TGNBRGYYTKNQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.