readPandas() header check throwing error

terraswat commented 6 years ago

Verana was looking for why her data file was throwing errors and it turned out to be our header-checking code in utils.py:readPandas(). She says:

I tried to change the read_csv command inside the readPandas function:

I included 'low_memory=False' -> did not work, ran out of memory
I included 'dtype=float' -> did not work, the first line is text
I changed the header option to 'header=0' and commented out the code following that checks for a header -> worked!

Interesting that the low_memory flag seemed to do the opposite of what it should.

terraswat commented 6 years ago

This was on a file with what appears to have a proper header:

/data/data/featureSpace/Treehouse/THPED_July2017/treehouse_public_samples_unique_hugo _log2_tpm_plus_1_expr_var_filtered.2017-08-11.tsv

mrJeppard commented 6 years ago

Closing due to inability to reproduce the error using the compute environment on hexcalc.

Stuartlab-UCSC / hexmap-view