Error

[vpandey-om]

AttributeError: 'NoneType' object has no attribute 'rows_for_cluster'

[weiju]

Hi, could you please provide a bit more context ? E.g. what version of Python rpy2/numpy/scipy you are using ? Also I would recommend turning off multiprocessing for your case as that might reveal more error information.

Thank you

[vpandey-om]

Hi Thank for reaching me. I am using python3.8 then I had to change rpy2 from the setup.py 'rpy2<=2.8.6' to rpy2 to get recent version of rpy2. I can install cMonkey2 successfully. Then I run this command to check bin/cmonkey2.sh --organism hal --rsat_base_url http://networks.systemsbiology.net/rsat example_data/hal/halo_ratios5.tsv It was always going through config_params['multiprocessing']=True and was giving that error. Now I went through config_params['multiprocessing']=False Now I am getting problem with this function Error( raise ValueError('Not an rpy2 R object and unable ' ValueError: Not an rpy2 R object and unable to map it into one: 0.25303088080736785 ) def density(kvalues, cluster_values, bandwidth, dmin, dmax): """generic function to compute density scores""" kwargs = {'bw': bandwidth, 'adjust': 2, 'from': dmin, 'to': dmax, 'n': 256, 'na.rm': True} import pdb; pdb.set_trace() rdens = robjects.r(""" rdens <- function(cluster_values, kvalues, ...) { d <- density(cluster_values, ...); p <- approx(d$x, rev(cumsum(rev(d$y))), kvalues)$y p / sum(p, na.rm=T) }""") return rdens(robjects.FloatVector(cluster_values), robjects.FloatVector(kvalues), **kwargs) Thank you very much for help me out !!! Best Vikash

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________________________________ From: Wei-ju Wu ***@***.***> Sent: 21 May 2021 20:15:34 To: baliga-lab/cmonkey2 Cc: Vikash Pandey; Author Subject: Re: [baliga-lab/cmonkey2] Error (#77) Hi, could you please provide a bit more context ? E.g. what version of Python rpy2/numpy/scipy you are using ? Also I would recommend turning off multiprocessing for your case as that might reveal more error information. Thank you — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#77 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AON75ZRRVC4T5HV34IHDDR3TO2PMNANCNFSM45JAP32Q>.

[vpandey-om]

________________________________ From: Vikash Pandey Sent: 21 May 2021 21:58:58 To: baliga-lab/cmonkey2; baliga-lab/cmonkey2 Cc: Author Subject: Re: [baliga-lab/cmonkey2] Error (#77) Hi Thank for reaching me. I am using python3.8 then I had to change rpy2 from the setup.py 'rpy2<=2.8.6' to rpy2 to get recent version of rpy2. I can install cMonkey2 successfully. Then I run this command to check bin/cmonkey2.sh --organism hal --rsat_base_url http://networks.systemsbiology.net/rsat example_data/hal/halo_ratios5.tsv It was always going through config_params['multiprocessing']=True and was giving that error. Now I went through config_params['multiprocessing']=False Now I am getting problem with this function Error( raise ValueError('Not an rpy2 R object and unable ' ValueError: Not an rpy2 R object and unable to map it into one: 0.25303088080736785 ) def density(kvalues, cluster_values, bandwidth, dmin, dmax): """generic function to compute density scores""" kwargs = {'bw': bandwidth, 'adjust': 2, 'from': dmin, 'to': dmax, 'n': 256, 'na.rm': True} import pdb; pdb.set_trace() rdens = robjects.r(""" rdens <- function(cluster_values, kvalues, ...) { d <- density(cluster_values, ...); p <- approx(d$x, rev(cumsum(rev(d$y))), kvalues)$y p / sum(p, na.rm=T) }""") return rdens(robjects.FloatVector(cluster_values), robjects.FloatVector(kvalues), **kwargs) Thank you very much for help me out !!! Best Vikash

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________________________________ From: Wei-ju Wu ***@***.***> Sent: 21 May 2021 20:15:34 To: baliga-lab/cmonkey2 Cc: Vikash Pandey; Author Subject: Re: [baliga-lab/cmonkey2] Error (#77) Hi, could you please provide a bit more context ? E.g. what version of Python rpy2/numpy/scipy you are using ? Also I would recommend turning off multiprocessing for your case as that might reveal more error information. Thank you — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#77 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AON75ZRRVC4T5HV34IHDDR3TO2PMNANCNFSM45JAP32Q>. beautifulsoup4==4.9.3 biopython==1.78 bleach==3.2.1 certifi==2020.12.5 cffi==1.14.5 chardet==4.0.0 cheroot==8.5.2 CherryPy==18.6.0 cherrypy-cors==1.6 cmonkey2==1.2.12 colorama==0.4.4 configparser==5.0.2 docutils==0.16 greenlet==1.1.0 httpagentparser==1.9.1 idna==2.10 jaraco.classes==3.2.1 jaraco.collections==3.3.0 jaraco.functools==3.3.0 jaraco.text==3.5.0 Jinja2==3.0.1 joblib==1.0.1 keyring==21.8.0 lxml==4.6.3 MarkupSafe==2.0.1 more-itertools==8.7.0 numpy==1.20.3 packaging==20.8 pandas==1.2.4 pkginfo==1.6.1 portend==2.7.1 pycparser==2.20 Pygments==2.7.3 pyparsing==2.4.7 python-dateutil==2.8.1 pytz==2021.1 readme-renderer==28.0 repoze.lru==0.7 requests==2.25.1 requests-toolbelt==0.9.1 rfc3986==1.4.0 Routes==2.5.1 rpy2==3.4.4 scikit-learn==0.24.2 scipy==1.6.3 six==1.16.0 soupsieve==2.2.1 SQLAlchemy==1.4.15 SQLAlchemy-Utils==0.37.3 svgwrite==1.4.1 tempora==4.0.2 threadpoolctl==2.1.0 twine==3.3.0 tzlocal==2.1 urllib3==1.26.2 webencodings==0.5.1 zc.lockfile==2.0

[weiju]

Thank you very much for this information ! Could you please update to cmonkey2 1.2.13, update your rpy2 version to 2.9.5 and let me know if that works for you ?

[vpandey-om]

Hi It is working with the given example. I want to run in plasmodiums and was wondering what should input should i give. (expression, fasta file, etc. ) It always genrate errors. Thank you. Best Vikash

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________________________________ From: Wei-ju Wu ***@***.***> Sent: 22 May 2021 00:04:39 To: baliga-lab/cmonkey2 Cc: Vikash Pandey; Author Subject: Re: [baliga-lab/cmonkey2] Error (#77) Thank you very much for this information ! Could you please update to cmonkey2 1.2.13, update your rpy2 version to 2.9.5 and let me know if that works for you ? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#77 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AON75ZWW6JEP5GRMGKMXXQ3TO3KHPANCNFSM45JAP32Q>.

[weiju]

Hi,
it would be helpful to provide any relevant error information you see. Most errors will be due to incomplete data, e.g. mapping information. Since cmonkey2 relies a lot on RSAT database information, the first task would be making sure that the organism you use is correctly mapped to an existing RSAT entry.

I can provide further assistance, but would need more information about e.g. the look of your gene identifiers and what particular plasmodium you are using (e.g. vivax, falciparum...)

[vpandey-om]

Hi, Thank you !!! You are true !!! I am using Plasmodium Berghei and there is no entry in the RSAT database. Can I handle 6000*30000 expression data for biclustering ? We don't have so much information about motifs for berghei. I was wondering how the software will execute cis regulatory associations. Thank you very much !!! Best Vikash

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________________________________ From: Wei-ju Wu ***@***.***> Sent: 24 May 2021 17:24:57 To: baliga-lab/cmonkey2 Cc: Vikash Pandey; Author Subject: Re: [baliga-lab/cmonkey2] Error (#77) Hi, it would be helpful to provide any relevant error information you see. Most errors will be due to incomplete data, e.g. mapping information. Since cmonkey2 relies a lot on RSAT database information, the first task would be making sure that the organism you use is correctly mapped to an existing RSAT entry. I can provide further assistance, but would need more information about e.g. the look of your gene identifiers and what particular plasmodium you are using (e.g. vivax, falciparum...) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#77 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AON75ZVPAGKLTLVSNXOD3C3TPJVUTANCNFSM45JAP32Q>.