Re: [mamba-help] ASE error

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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...
> 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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