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ncsa / NEAT

NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.
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Error with utilities/vcf_compare_OLD.py #39

Closed jkalleberg closed 2 years ago

jkalleberg commented 2 years ago

Describe the bug I ran python ~/NEAT/utilities/vcf_compare_OLD.py --help to confirm that downloading the git repo worked. However, I got the following error that seems to indicate a bug in the argument parser of this script. 

(neat_conda) python ~/NEAT/utilities/vcf_compare_OLD.py 
Traceback (most recent call last):
  File "/storage/hpc/group/UMAG_test/WORKING/jakth2/deep-variant/scripts/setup/NEAT/utilities/vcf_compare_OLD.py", line 37, in <module>
    parser = argparse.ArgumentParser('python %prog [options] -r <ref.fa> -g <golden.vcf> -w <workflow.vcf>',
TypeError: __init__() got an unexpected keyword argument 'version'

To Reproduce Steps to reproduce the behavior:

  1. cd /path/to/working/directory
  2. conda activate -p /path/to/neat_environment with packages listed as Requirements
  3. git clone https://github.com/ncsa/NEAT.git
  4. cd NEAT
  5. pip install . 
    ... 
Successfully installed NEAT-3.0
  6. See error

Expected behavior

python vcf_compare_OLD.py
        -r <ref.fa>        * Reference Fasta                           \
        -g <golden.vcf>    * Golden VCF                                \
        -w <workflow.vcf>  * Workflow VCF                              \
        -o <prefix>        * Output Prefix                             \
        -m <track.bed>     Mappability Track                           \
        -M <int>           Maptrack Min Len                            \
        -t <regions.bed>   Targetted Regions                           \
        -T <int>           Min Region Len                              \
        -c <int>           Coverage Filter Threshold [15]              \
        -a <float>         Allele Freq Filter Threshold [0.3]          \
        --vcf-out          Output Match/FN/FP variants [False]         \
        --no-plot          No plotting [False]                         \
        --incl-homs        Include homozygous ref calls [False]        \
        --incl-fail        Include calls that failed filters [False]   \
        --fast             No equivalent variant detection [False]

Desktop (please complete the following information):

joshfactorial commented 2 years ago

I pulled in your changes. We're planning to overhaul vcf_compare once we get gen_reads updated.

jkalleberg commented 2 years ago

I figured an overhaul was coming, but thanks for the update!