Re: [mamba-help] ASE error

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

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)
>
>
>
>
>
>
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