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blachlylab / mucor

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Pandas.DataFrame.to_csv() unexpected argument sparsify #12

Open kwkroll32 opened 7 years ago

kwkroll32 commented 7 years ago

Received an error writing vcf output. Apparently pandas.DataFrame.to_csv() doesn't accept the "sparsify" argument (anymore?). Not sure what it is supposed to do, but commenting it out stops the error and still produces a vcf file. If we can't remember where this came from, I propose we remove that argument from this particular to_csv call.

Pandas 0.19.1 See the offending line in output.VCF here

Traceback (most recent call last):
  File "/home/karl/Tools/mucor/mucor.py", line 699, in 
    main()
  File "/home/karl/Tools/mucor/mucor.py", line 690, in main
    printOutput(config, str(config.outputDir), varDF)
  File "/home/karl/Tools/mucor/mucor.py", line 649, in printOutput
    ow.write(varDF,format,outputDirName,config)
  File "/home/karl/Tools/mucor/output.py", line 95, in write
    self.supported_formats[format]()
  File "/home/karl/Tools/mucor/output.py", line 399, in VCF
    out.to_csv(ofVariantVCF, sep='\t', na_rep='?', index=False, header=True, sparsify=False)
TypeError: to_csv() got an unexpected keyword argument 'sparsify'
jblachly commented 7 years ago

I can’t even find this parameter in the OLD version of pandas documentation. . Probably was undocumented parameter — how did you even find it? . Agree with removing but need to figure out what it will do. pandas manual has a section of sparsified data structures. HAs to do , I think, with multi-indices.

On Feb 4, 2017, at 10:46 AM, Karl notifications@github.com wrote:

Received an error writing vcf output. Apparently pandas.DataFrame.to_csv() doesn't accept the "sparsify" argument (anymore?). Not sure what it is supposed to do, but commenting it out stops the error and still produces a vcf file. If we can't remember where this came from, I propose we remove that argument from this particular to_csv call.

Pandas 0.19.1 See the offending line in output.VCF here https://github.com/blachlylab/mucor/blob/master/output.py#L399 Traceback (most recent call last): File "/home/karl/Tools/mucor/mucor.py", line 699, in main() File "/home/karl/Tools/mucor/mucor.py", line 690, in main printOutput(config, str(config.outputDir), varDF) File "/home/karl/Tools/mucor/mucor.py", line 649, in printOutput ow.write(varDF,format,outputDirName,config) File "/home/karl/Tools/mucor/output.py", line 95, in write self.supported_formats[format]() File "/home/karl/Tools/mucor/output.py", line 399, in VCF out.to_csv(ofVariantVCF, sep='\t', na_rep='?', index=False, header=True, sparsify=False) TypeError: tocsv() got an unexpected keyword argument 'sparsify' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/blachlylab/mucor/issues/12, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFtbUUlYqinAfJznR-WcVEoQOcUm1Mxks5rZJ05gaJpZM4L3Lvo>.

kwkroll32 commented 7 years ago

I got that error by simply trying to write vcf output. Something about my current environment must be different than before - Pandas 0.17 vs 0.19 maybe?