gff3_fix error

[Rhinogradentia]

Hi,

I tried to run gff3_fix an ran in following error

Before I of course ran QC:

gff3_QC -g in.gff3 -f in.fasta -i -o QC-Check.out -s QC_Check.stats

Afterwards I extracted only the wrong phases into wrongPhase.out

grep "Wrong phase"  QC-Check.out > wrongPhase.out

It looks like this:

head wrongPhase.out
Line_num        Error_code      Error_level     Error_tag
['Line 1030']   Ema0006 Info    [Wrong phase 1, should be 0]
['Line 1102']   Ema0006 Info    [Wrong phase 2, should be 0]
['Line 2797']   Ema0006 Info    [Wrong phase 1, should be 0]
['Line 3384']   Ema0006 Info    [Wrong phase 0, should be 1]
['Line 3408']   Ema0006 Info    [Wrong phase 2, should be 0]
['Line 3414']   Ema0006 Info    [Wrong phase 0, should be 1]
['Line 3504']   Ema0006 Info    [Wrong phase 1, should be 2]
['Line 3528']   Ema0006 Info    [Wrong phase 1, should be 0]
['Line 3530']   Ema0006 Info    [Wrong phase 0, should be 1]
['Line 3552']   Ema0006 Info    [Wrong phase 2, should be 0]

Then running gff3_fix:

gff3_fix -qc_r wrongPhase.out -g in.gff3 -og out.gff3
INFO     Checking QC report file (wrongPhase.out)...
INFO     Checking GFF3 file (in.gff3)...
INFO     Reading QC report file: (wrongPhase.out)...

INFO     Reading GFF3 file: (in.gff3)...

Traceback (most recent call last):
  File "/home/user/.local/bin/gff3_fix", line 8, in <module>
    sys.exit(script_main())
  File "/home/user/.local/lib/python3.10/site-packages/gff3tool/bin/gff3_fix.py", line 95, in script_main
    gff3_fix.fix.main(gff3=gff3, output_gff=args.output_gff, error_dict=error_dict, line_num_dict=line_num_dict, logger=logger_stderr)
  File "/home/user/.local/lib/python3.10/site-packages/gff3tool/lib/gff3_fix/fix.py", line 686, in main
    fix_phase(gff3=gff3, error_list=error_dict[error_code], line_num_dict=line_num_dict, logger=logger)
  File "/home/user/.local/lib/python3.10/site-packages/gff3tool/lib/gff3_fix/fix.py", line 424, in fix_phase
    phase = list(map(int,re.findall(r'\d',line_num_dict[sorted_CDS_list[0]['line_index']+1]['Ema0006']))[1])
TypeError: 'map' object is not subscriptable

The error stays the same when the complete report file is input.

I'm running this in a conda environment :

python --version
Python 3.12.0

Also tried it in a non-conda environment:

python --version
Python 2.7.18

gff3_fix --version
gff3_fix 2.1.0

gff3_QC --version
gff3_QC 2.1.0

What could be the problem here? Thank you a lot in advance.
Best,
Nadine

[mpoelchau]

Thanks for reaching out @Rhinogradentia . I can't see anything wrong with your wrongPhase.out file. I'm curious whether the python3 version is too high - could you try the same command in a conda environment with python 3.7?

If that doesn't work, it would be great if you could attach the gff3 and fasta files so I can troubleshoot, or email them to i5k@ars.usda.gov

[Rhinogradentia]

Hi,

I found time to test it with python 3.7 - ther same error occurs. Unfortunately I can't share the input files at the moment. I will try to find the source of the error myself.

# fresh install conda environment with python 3.7
 conda create --name py3.7 python=3.7
source activate py3.7
(py3.7) user $ pip install gff3tool
/home/user/miniconda3/envs/py3.7/bin/gff3_fix

python --version
Python 3.7.12

gff3_fix -qc_r WrongPhase.txt -g in.gff3 -og out.gff3
INFO     Checking QC report file (WrongPhase.txt)...
INFO     Checking GFF3 file (in.gff3)...
INFO     Reading QC report file: (WrongPhase.txt)...

INFO     Reading GFF3 file: (in.gff3)...

Traceback (most recent call last):
  File "/home/user/.local/bin/gff3_fix", line 8, in <module>
    sys.exit(script_main())
  File "/home/user/.local/lib/python3.10/site-packages/gff3tool/bin/gff3_fix.py", line 95, in script_main
    gff3_fix.fix.main(gff3=gff3, output_gff=args.output_gff, error_dict=error_dict, line_num_dict=line_num_dict, logger=logger_stderr)
  File "/home/user/.local/lib/python3.10/site-packages/gff3tool/lib/gff3_fix/fix.py", line 686, in main
    fix_phase(gff3=gff3, error_list=error_dict[error_code], line_num_dict=line_num_dict, logger=logger)
  File "/home/user/.local/lib/python3.10/site-packages/gff3tool/lib/gff3_fix/fix.py", line 424, in fix_phase
    phase = list(map(int,re.findall(r'\d',line_num_dict[sorted_CDS_list[0]['line_index']+1]['Ema0006']))[1])
TypeError: 'map' object is not subscriptable

Thanks for trying to help.

Best,
Nadine

[jacopoM28]

Hello @Rhinogradentia,

did you find a solution at the end? I am having the same issue.

Best,
Jacopo

[Rhinogradentia]

Hi,
Unfortunately, no - I think I used something else or solved my problem differently in the end.

Best,
Nadine