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PMBio / limix-backup

http://pmbio.github.io/limix/
Apache License 2.0
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limix_converter problem with phenotype_sample.csv #17

Open alexd106 opened 8 years ago

alexd106 commented 8 years ago

Hi

Iam having a problem following the 'loading files into LIMIX' tutorial, specifically with using limix_converter to convert the phenotype_sample.csv into hdf5 format.

This is the command Iam using :

limix_converter --outfile=./my_pheno.hdf5 -csv=./phenotype_sample.csv

It seems to run ok, but the hdf5 file does not contain any datasets or groups.

h5dump -A my_pheno.hdf5 
HDF5 "my_pheno.hdf5" {
GROUP "/" {
}
}

I am using this on a biolinux box Linux XXX 3.13.0-68-generic #111-Ubuntu SMP Fri Nov 6 18:17:06 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

and using LIMIX version limix==0.7.12 installed using pip.

I have also tried using my own phenotype file (.csv) but have the same problem.
Can anyone shed any light? Cheers Alex

alexd106 commented 8 years ago

Ok, i sorted the problem. There is a typo in the tutorial 

limix_converter --outfile=./my_file.hdf5 -csv=./phenotype_sample.csv

should read 

limix_converter --outfile=./my_file.hdf5 --csv=./phenotype_sample.csv

note double '-' for the csv argument. Sorry, should have spotted that.

I do however get another warning

/usr/local/lib/python2.7/dist-packages/limix/io/conversion.py:78: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support sep=None with delim_whitespace=False; you can avoid this warning by specifying engine='python'.
  C = pandas.io.parsers.read_csv(csv_file,sep=sep,header=None,index_col=False,*args,**kw_args)

but it seems to convert to hdf5 ok. Thanks Alex

alexd106 commented 8 years ago

Ok, in case anyone else comes across this I bypassed the warning by including the -D option 

limix_converter -O ./my_pheno.hdf5 -C ./phenotype_sample.csv -D ,