cmapPy

cmapPy copied to clipboard

Cannot write back GCT file that has been parsed

1

I am trying to do just a simple test of reading in an already existing GCT file and then writing it back but this fails. The same GCT file works...

Munchic

Bug .GCT written by cmapPy on Windows have inconsistent line endings

4

Hi Lev, #Bug .GCT files written with cmapPy on Windows, show alternating blank lines after the top 3 lines when opened in Excel, though fine in code editor Spyder v5.12.3...

KarlClauser

parse_gctx takes too much memory when we inquire specific columns and rows

2

When loading a very large gctx file ~24Gb on my laptop with 16 Gb using the function `cmapPy.pandasGEXpress.parse.parse`, I run out of memory with the following error: `Unable to allocate...

Dom303

I am trying to install cmappy following the instructions in this repo with the current anconda: `conda create --name my_cmapPy_env -c bioconda python=2.7.11 numpy=1.11.2 pandas=0.20.3 h5py=2.7.0 requests==2.13.0 cmappy ` ,...

antonkratz

Subsetting picks wrong dimension to subset over first

1

There is some logic in parse_data_df (pasted below) that attempts to pick the best dimension to subset over first, but it isn't quite right. ```python def parse_data_df(data_dset, ridx, cidx, row_meta,...

darintay

when I tried to parse the cmap2020, there were errors as follow: Traceback (most recent call last): File "get_gct.py", line 17, in get_gct() File "get_gct.py", line 13, in get_gct goo...

DeepColin

Here is the code I'm using: `import cmapPy.pandasGEXpress.parse_gctx as parse_gctx import time from threading import Thread res = [] threads = [] def read(idx): print(f'Start reading {idx}') t = time.time()...

nborunov-integral

Error during parsing

3

I'm trying to read a gctx file downloaded from https://clue.io/data. This is my code: `from cmapPy.pandasGEXpress.parse_gct import parse` `from cmapPy.pandasGEXpress.write_gct import write` `parse("C:/Users/User/Desktop/gctx/testdatan1000978.gctx")` This is the error: `(base) C:\Users\User\Desktop\hello>D:/anaconda/python.exe c:/Users/User/Desktop/gctx/readgcxtx.py`...

LeskosekRok

I'm trying to open the notebook in my browser but it doesn't open! cmapPy/tutorials/cmapPy_pandasGEXpress_tutorial.ipynb Can you fix this, please? Thanks, Denise

deniseduma

reading gctx from a non-fs file object

1

Hi, In our settings there is often a need to read a `.gctx` file from a non-file (i.e. python file object). Currently it is not possible with cmapPy. The parse...

idavydov