firasmidani
commented
1 year ago Thank you for sharing the command and error trace, it's quite helpful.
Based on your command, it seems that Fit_pool_summary.tx should have a column called Control and you are trying to normalize your data based on this column.
If you use the normalize function and do not call the --normalize-by argument, then, AMiGA will use the Control column by default. If you would still like to be explicit and call the --normalize-by argument, you will need to tell AMiGA which column in your summary file distinguish treatments and control (e.g. Control column) but you also need to tell AMiGA which value in the Control column corresponds to your control wells/conditions (e.g. Control:1). So, you can do either of the following commands:
option 1
Here, I specify which value in the Control column corresponds to control wells by including ":1" in the normalize-by value
C:\Users\ofm83\Documents\Projects_python\amiga-master>python amiga.py normalize --input C:\Users\ofm83\Documents\A.baumannii_amiga\summary\Fit_pool_summary.txt --group-by "Isolate" --normalize-method "division" --normalize-by "Control:1" --verboseoption 2
Here, we assume that your control rows/wells have values of 1 in the Control column (this is the default behavior by AMiGA), so we do not use the --normalize-by argument at all.
C:\Users\ofm83\Documents\Projects_python\amiga-master>python amiga.py normalize --input C:\Users\ofm83\Documents\A.baumannii_amiga\summary\Fit_pool_summary.txt --group-by "Isolate" --normalize-method "division" --verboseTry these out and let me know if you are still having this issue.
ofleitas
Hello I am trying to normalize my pooled data by division, but I got an error message.
C:\Users\ofm83\Documents\Projects_python\amiga-master>python amiga.py normalize --input C:\Users\ofm83\Documents\A.baumannii_amiga\summary\Fit_pool_summary.txt --group-by "Isolate" --normalize-method "division" --normalize-by "Control" --ve rbose
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User provided the following command-line arguments:
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input...............C:\Users\ofm83\Documents\A.baumannii_amiga\summary\Fit_pool_summary.txt over_write..........False verbose.............True group_by............Isolate normalize_by........Control normalize_method....division
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AMiGA is parsing your file(s)
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Traceback (most recent call last): File "amiga.py", line 400, in
AMiGA()
File "amiga.py", line 90, in init
getattr(self, args.command)()
File "amiga.py", line 304, in normalize
normalize(args)
File "C:\Users\ofm83\Documents\Projects_python\amiga-master\libs\normalize.py", line 56, in main
df = normalizeParameters(args,df)
File "C:\Users\ofm83\Documents\Projects_python\amiga-master\libs\normalize.py", line 115, in normalizeParameters
controlby = checkParameterCommand(args.normalize_by)
File "C:\Users\ofm83\Documents\Projects_python\amiga-master\libs\interface.py", line 132, in checkParameterCommand
lines_values = [[jj.strip() for jj in re.split(sep,ii.split(':')[1])] for ii in lines]
File "C:\Users\ofm83\Documents\Projects_python\amiga-master\libs\interface.py", line 132, in
lines_values = [[jj.strip() for jj in re.split(sep,ii.split(':')[1])] for ii in lines]
IndexError: list index out of range
C:\Users\ofm83\Documents\Projects_python\amiga-master>