Index contains duplicate entries, cannot reshape
aassie opened this issue · comments
Hello Firas,
Thank you for developing this nice tool.
If I run basic commands the tool appears to work, it generated nice figures for our plates and a summary table.
However, when I try to pool my replicates, I have the following error:
python ~/Documents/Tools/amiga/amiga.py -i ./Run1/ -o "pooled_analysis" --pool-by "Isolate"
#-----------------------------------------------#
# AMiGA is peeking inside the working directory #
#-----------------------------------------------#
#-------------------------------------------------------------#
# AMiGA is parsing command-line arguments and parameter files #
#-------------------------------------------------------------#
#------------------------------------------#
# AMiGA is parsing and cleaning data files #
#------------------------------------------#
#--------------------------------------------#
# AMiGA is parsing and reading mapping files #
#--------------------------------------------#
#----------------------------------------------------------#
# AMiGA is preparing or analyzing data based on user input #
#----------------------------------------------------------#
#--------------------------------#
# AMiGA is fitting growth curves #
#--------------------------------#
Traceback (most recent call last):
File "/Users/adrien/Documents/Tools/amiga/amiga.py", line 75, in <module>
runGrowthFitting(data,mappings,directory,args,verbose=args['verbose'])
File "/Users/adrien/Documents/Tools/amiga/libs/analyze.py", line 137, in runGrowthFitting
runCombinedGrowthFitting(data,mapping,directory,args,verbose=verbose)
File "/Users/adrien/Documents/Tools/amiga/libs/analyze.py", line 285, in runCombinedGrowthFitting
gm = GrowthModel(df=cond_data,ARD=True,heteroscedastic=fix_noise,nthin=nthin)#,
File "/Users/adrien/Documents/Tools/amiga/libs/model.py", line 104, in __init__
sub_df = describeVariance(sub_df,time='Time',od='OD')
File "/Users/adrien/Documents/Tools/amiga/libs/model.py", line 52, in describeVariance
tmp = pd.pivot(df,index=time,columns='SID',values=od)
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/pivot.py", line 430, in pivot
return indexed.unstack(columns)
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/series.py", line 3748, in unstack
return unstack(self, level, fill_value)
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/reshape.py", line 418, in unstack
unstacker = _Unstacker(
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/reshape.py", line 142, in __init__
self._make_selectors()
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/reshape.py", line 180, in _make_selectors
raise ValueError("Index contains duplicate entries, " "cannot reshape")
ValueError: Index contains duplicate entries, cannot reshape
Any idea what causes it?
This is how my metadata files look like:
head Run1/mapping/*.txt
==> Run1/mapping/LB_1.txt <==
Isolate Group Control Replicate
A1 mut1 1 0 1
A2 mut2 1 0 1
==> Run1/mapping/LB_2.txt <==
Isolate Group Control Replicate
A1 mut1 1 0 2
A2 mut2 1 0 2
==> Run1/mapping/M9_1.txt <==
Isolate Group Control Replicate
A1 mut1 2 0 1
A2 mut2 2 0 1
==> Run1/mapping/M9_2.txt <==
Isolate Group Control Replicate
A1 mut1 2 0 2
A2 mut2 2 0 2
Thank you for your help,
Adrien
Hi Adrien,
Did you create your own metadata files?
If yes, what happens if you include a "Plate_ID" column for each mapping
file (as I show for example below)?
==> Run1/mapping/M9_2.txt <==
Plate_ID Isolate Group Control Replicate
A1 M9_2 mut1 2 0 2
A2 M9_2 mut2 2 0 2
Firas
…On Fri, Feb 12, 2021 at 9:18 AM Adrien Assie ***@***.***> wrote:
Hello Firas,
Thank you for developing this nice tool.
If I run basic commands the tool appears to work, it generated nice
figures for our plates and a summary table.
However, when I try to pool my replicates, I have the following error:
python ~/Documents/Tools/amiga/amiga.py -i ./Run1/ -o "pooled_analysis" --pool-by "Isolate"
#-----------------------------------------------#
# AMiGA is peeking inside the working directory #
#-----------------------------------------------#
#-------------------------------------------------------------#
# AMiGA is parsing command-line arguments and parameter files #
#-------------------------------------------------------------#
#------------------------------------------#
# AMiGA is parsing and cleaning data files #
#------------------------------------------#
#--------------------------------------------#
# AMiGA is parsing and reading mapping files #
#--------------------------------------------#
#----------------------------------------------------------#
# AMiGA is preparing or analyzing data based on user input #
#----------------------------------------------------------#
#--------------------------------#
# AMiGA is fitting growth curves #
#--------------------------------#
Traceback (most recent call last):
File "/Users/adrien/Documents/Tools/amiga/amiga.py", line 75, in <module>
runGrowthFitting(data,mappings,directory,args,verbose=args['verbose'])
File "/Users/adrien/Documents/Tools/amiga/libs/analyze.py", line 137, in runGrowthFitting
runCombinedGrowthFitting(data,mapping,directory,args,verbose=verbose)
File "/Users/adrien/Documents/Tools/amiga/libs/analyze.py", line 285, in runCombinedGrowthFitting
gm = GrowthModel(df=cond_data,ARD=True,heteroscedastic=fix_noise,nthin=nthin)#,
File "/Users/adrien/Documents/Tools/amiga/libs/model.py", line 104, in __init__
sub_df = describeVariance(sub_df,time='Time',od='OD')
File "/Users/adrien/Documents/Tools/amiga/libs/model.py", line 52, in describeVariance
tmp = pd.pivot(df,index=time,columns='SID',values=od)
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/pivot.py", line 430, in pivot
return indexed.unstack(columns)
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/series.py", line 3748, in unstack
return unstack(self, level, fill_value)
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/reshape.py", line 418, in unstack
unstacker = _Unstacker(
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/reshape.py", line 142, in __init__
self._make_selectors()
File "/Users/adrien/anaconda3/envs/amiga/lib/python3.8/site-packages/pandas/core/reshape/reshape.py", line 180, in _make_selectors
raise ValueError("Index contains duplicate entries, " "cannot reshape")
ValueError: Index contains duplicate entries, cannot reshape
Any idea what causes it?
This is how my metadata files look like:
head Run1/mapping/*.txt
==> Run1/mapping/LB_1.txt <==
Isolate Group Control Replicate
A1 mut1 1 0 1
A2 mut2 1 0 1
==> Run1/mapping/LB_2.txt <==
Isolate Group Control Replicate
A1 mut1 1 0 2
A2 mut2 1 0 2
==> Run1/mapping/M9_1.txt <==
Isolate Group Control Replicate
A1 mut1 2 0 1
A2 mut2 2 0 1
==> Run1/mapping/M9_2.txt <==
Isolate Group Control Replicate
A1 mut1 2 0 2
A2 mut2 2 0 2
Thank you for your help,
Adrien
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Ah yes, it worked thank you very much!