ImportError during Figaro running

[luigallucci]

Hi all,

I'm trying to run figaro on a subset of samples. I'm facing this problems after running it with the following command set:

python3 figaro.py -i /Users/lgallucc/Desktop/Tempor/Luigi/ -o /Users/lgallucc/Desktop/TemporLuigi/Figaro -a 320 -f 20 -r 20

Traceback (most recent call last):
  File "/Users/lgallucc/figaro/figaro/figaro.py", line 4, in <module>
    from . import environmentParameterParser, fileNamingStandards, fastqAnalysis, trimParameterPrediction
ImportError: attempted relative import with no known parent package

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/lgallucc/figaro/figaro/trimParameterPrediction.py", line 4, in <module>
    from . import fileNamingStandards
ImportError: attempted relative import with no known parent package

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/lgallucc/figaro/figaro/figaro.py", line 6, in <module>
    import environmentParameterParser, fileNamingStandards, fastqAnalysis, trimParameterPrediction
  File "/Users/lgallucc/figaro/figaro/trimParameterPrediction.py", line 9, in <module>
    import fileNamingStandards, fastqHandler, fastqAnalysis, expectedErrorCurve
  File "/Users/lgallucc/figaro/figaro/expectedErrorCurve.py", line 13, in <module>
    class ExponentialFit(object):
  File "/Users/lgallucc/figaro/figaro/expectedErrorCurve.py", line 17, in ExponentialFit
    def __init__(self, a:float, b:float, c:float, covariance:collections.Iterable = None, rSquared:float = None, curvePNG:str=None):
AttributeError: module 'collections' has no attribute 'Iterable'

[nvpatin]

I am getting the same error, running Figaro on Mac OS 13.4.1 and Python 3.6. This also happens with higher Python versions (3.8 and 3.10).

[hjarnek]

This is because since Python 3.3 the collections module has been succeeded by the collections.abc module. You can fix this by simply find&replace all instances of "collections" with "collections.abc" in all Figaro Python scripts that contain this module.

Figaro is not maintained anymore though. There has been some rumours about an update called Figaro2 for a long time, but not from Zymo.

[ayoraind]

Thank you very much @hjarnek. Your suggestion bailed me out today. It worked!