Quast 5.0.2 Problem

Question

[augustofranco93]

Hi everyone,

I'm trying to run quast with python ./setup.py test to verify installation. And then it shows this error.

module 'cgi' has no attribute 'escape'
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/quast-5.0.2-py3.8.egg/EGG-INFO/scripts/quast.py", line 307, in <module>
    return_code = main(sys.argv[1:])
  File "/usr/local/lib/python3.8/dist-packages/quast-5.0.2-py3.8.egg/EGG-INFO/scripts/quast.py", line 148, in main
    from quast_libs import basic_stats
  File "/usr/local/lib/python3.8/dist-packages/quast-5.0.2-py3.8.egg/quast_libs/basic_stats.py", line 15, in <module>
    from quast_libs.circos import set_window_size
  File "/usr/local/lib/python3.8/dist-packages/quast-5.0.2-py3.8.egg/quast_libs/circos.py", line 25, in <module>
    from quast_libs.icarus_utils import get_assemblies, check_misassembled_blocks, Alignment
  File "/usr/local/lib/python3.8/dist-packages/quast-5.0.2-py3.8.egg/quast_libs/icarus_utils.py", line 15, in <module>
    from quast_libs.html_saver.html_saver import trim_ref_name
  File "/usr/local/lib/python3.8/dist-packages/quast-5.0.2-py3.8.egg/quast_libs/html_saver/html_saver.py", line 18, in <module>
    from quast_libs.site_packages.jsontemplate import jsontemplate
  File "/usr/local/lib/python3.8/dist-packages/quast-5.0.2-py3.8.egg/quast_libs/site_packages/jsontemplate/jsontemplate.py", line 583, in <module>
    'html': cgi.escape,
AttributeError: module 'cgi' has no attribute 'escape'
ERROR! exception caught!

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[bstrope15]

If you open up the file jsontemplate.py, that is where the error is occurring:

You will first need to 'import html' somewhere near the beginning of the script, preferably where the other modules are imported. Then at line 583, replace "cgi.escape" to "html.escape"

[horeyezonr]

Thank you, it worked for me!