[mamba-help] ASE error

[Alexandros D. <dim...@fl...>]

Dear Dr. Rivas,

After using the GATK ASEReadCounter walker on my data, I was directed to 
the MAMBA software for allele-specific expression analysis.
I have downloaded and successfully installed MAMBA but I cannot make it 
execute the ASE example. I have downloaded both the small asetest.txt.gz 
example and the much larger GEUVADIS ASE file 
GD462.ASE.COV8.ANNOT_PTV.txt.gz. However, when I give the command

mamba --module ASE --fileout asetest.txt.gz --nt 1 --grep 
"include|exclude|freqthreshold"  --verbosity CRITICAL

I get an error:

/home/dimopoulos/anaconda/lib/python2.7/site-packages/pandas/rpy/__init__.py:11: 
FutureWarning: The pandas.rpy module is deprecated and will be removed 
in a future version. We refer to external packages like rpy2.
See here for a guide on how to port your code to rpy2: 
http://pandas.pydata.org/pandas-docs/stable/r_interface.html
   FutureWarning)
Traceback (most recent call last):
   File "/home/dimopoulos/anaconda/bin/mamba", line 8, in <module>
     load_entry_point('mamba==1.0.0', 'console_scripts', 'mamba')()
   File "build/bdist.linux-x86_64/egg/mamba/MAMBAWrapper.py", line 214, 
in main
   File "build/bdist.linux-x86_64/egg/mamba/MAMBAWrapper.py", line 249, 
in runModule
   File "build/bdist.linux-x86_64/egg/mamba/ASE.py", line 969, in main
ValueError: could not convert string to float: freqthreshold

if I remove the --grep "include|exclude|freqthreshold" part of the 
command I still get an error:

mamba --module ASE --fileout asetest.txt.gz --nt 1  --verbosity CRITICAL

/home/dimopoulos/anaconda/lib/python2.7/site-packages/pandas/rpy/__init__.py:11: 
FutureWarning: The pandas.rpy module is deprecated and will be removed 
in a future version. We refer to external packages like rpy2.
See here for a guide on how to port your code to rpy2: 
http://pandas.pydata.org/pandas-docs/stable/r_interface.html
   FutureWarning)
Traceback (most recent call last):
   File "/home/dimopoulos/anaconda/bin/mamba", line 8, in <module>
     load_entry_point('mamba==1.0.0', 'console_scripts', 'mamba')()
   File "build/bdist.linux-x86_64/egg/mamba/MAMBAWrapper.py", line 214, 
in main
   File "build/bdist.linux-x86_64/egg/mamba/MAMBAWrapper.py", line 249, 
in runModule
   File "build/bdist.linux-x86_64/egg/mamba/ASE.py", line 947, in main
AttributeError: 'bool' object has no attribute 'split'

Do you have any suggestions on what I might be doing wrong?

Thank you in advance for your time,

Alexandros Dimopoulos

Post Doctoral Fellow
Biomedical Sciences Research Center “Alexander Fleming”
Institute of Molecular Biology & Genetics
Vari, 16672
Athens, Greece
+30-210-9656310 (ext. 144)