Re: [mamba-help] ASE error
Brought to you by:
mrivasbroad
|
From: Alexandros D. <dim...@fl...> - 2015-10-05 13:49:35
|
Thank you for your help! On 04/10/15 11:31, Manuel Rivas wrote: > Hello Alexandros - Please read the following section: > > > Application to simulated dataset. > > We simulated ASE data for 300 variants and 3 tissues. RNA-seq coverage > is simulated as a Poisson distribution > <http://en.wikipedia.org/wiki/Poisson_distribution> with expected > coverage of 30,20, and 40 for each tissue. > > A 67%, 23%, 10% mixture dataset with θ= .8, .5, .95 (binomial > distribution <http://en.wikipedia.org/wiki/Binomial_distribution>) was > generated. > > To apply the models we run mamba as follows > > mamba --module ASE --fileout asetest.txt.gz --nt 2 --seed 10 --grep ">,0,=STOP_GAINED|DFGFDG" --niter 100 --burn 10 > > where |--niter [int]| and |--burn [int]| are the number of iterations > and burn-in period for the Gibbs sampler, respectively. > > Results from the GTM and the GTM* (when multiple tissues are > available) are generated. GTM estimates: > > NOASE MODASE SNGASE HET0 HET1 > 1 0.2166671 0.6467365 0.08923985 0.02666694 0.02068966 > Whereas GTM* estimates: > est low95 up95 > NOASE 0.226645280 0.1887562079 0.27998550 > MODASE 0.664520022 0.5992223252 0.71721846 > SNGASE 0.094709155 0.0621824885 0.12861006 > HET0 0.004789438 0.0001708784 0.01900929 > HET1 0.009336103 0.0004127940 0.03151795 > with tissue-specificity estimate: > est low95 up95 > TIS_SPE 0.006466667 0.00 0.01553708 > > On Thu, Oct 1, 2015 at 5:23 AM, Alexandros Dimopoulos > <dim...@fl... <mailto:dim...@fl...>> wrote: > > 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) > > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > mambas-help mailing list > mam...@li... > <mailto:mam...@li...> > https://lists.sourceforge.net/lists/listinfo/mambas-help > > |