search

precimed / python_convert

A collection of various utilities for GWAS summary statistics
GNU General Public License v3.0
26 stars 11 forks source link

Error report when using fdrmat2csv.py: Length of values does not match length of index #38

Open WQ-CHENG opened 4 years ago

WQ-CHENG commented 4 years ago

Here are the details:

python /opt/python_convert/fdrmat2csv.py result.mat 9279485_ref.bim
Load result.mat
Load 9279485_ref.bim
/opt/python_convert/fdrmat2csv.py:14: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
  ref=pd.read_table(reffile, delim_whitespace=True)
Traceback (most recent call last):
  File "/opt/python_convert/fdrmat2csv.py", line 15, in <module>
    ref['FDR']=sumstats['fdrmat']
  File "/usr/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3370, in __setitem__
    self._set_item(key, value)
  File "/usr/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3445, in _set_item
    value = self._sanitize_column(key, value)
  File "/usr/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3630, in _sanitize_column
    value = sanitize_index(value, self.index, copy=False)
  File "/usr/local/lib/python2.7/site-packages/pandas/core/internals/construction.py", line 519, in sanitize_index
    raise ValueError('Length of values does not match length of index')
ValueError: Length of values does not match length of index
ofrei commented 4 years ago

9279485_ref is deprecated, we've moved to 9545380_ref/9545380.ref It's unfortunate that both templates have ~9M SNPs. The one with 9.5M correct. The one with 9.2M is legacy (deprecated)

On Mon, Mar 30, 2020 at 4:05 PM W.Q.CHENG notifications@github.com wrote:

  • python version: 2.7
  • 9279485_ref.bim downloaded from NIRD GWAS sumstats directory.
  • /result.mat was generated from pleioFDR.
  • python packages used in fdrmat2csv.py were already installed.

Here are the details:

python /opt/python_convert/fdrmat2csv.py result.mat 9279485_ref.bim Load result.mat Load 9279485_ref.bim /opt/python_convert/fdrmat2csv.py:14: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. ref=pd.read_table(reffile, delim_whitespace=True) Traceback (most recent call last): File "/opt/python_convert/fdrmat2csv.py", line 15, in ref['FDR']=sumstats['fdrmat'] File "/usr/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3370, in setitem self._set_item(key, value) File "/usr/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3445, in _set_item value = self._sanitize_column(key, value) File "/usr/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3630, in _sanitize_column value = sanitize_index(value, self.index, copy=False) File "/usr/local/lib/python2.7/site-packages/pandas/core/internals/construction.py", line 519, in sanitize_index raise ValueError('Length of values does not match length of index') ValueError: Length of values does not match length of index

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/precimed/python_convert/issues/38, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEPV6OWQ3DIZH5Y7CYEBGDRKCRJTANCNFSM4LWTUKRA .