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cmap / cmapPy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools
https://clue.io/cmapPy/index.html
BSD 3-Clause "New" or "Revised" License
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Error in opening LINCS L1000 .gctx file #83

Closed songsong0425 closed 12 months ago

songsong0425 commented 12 months ago

Hi, all. I'm in trouble while running the cmapPy for .gctx file. I've tried to open the .gctx file in L1000 Characteristic Direction Coefficient Tables following the tutorial code here. But I'm in trouble during the process because of the cmapPy package. Can you tell me how to open the .gctx file? Sorry for bothering you. This is the code that I tried:

from cmapPy.pandasGEXpress.parse import parse

my_col_metadata = parse("/home/xxx/yyy/Datasets/KG/LINCS_L1000/siRNA_coeff_mat.gctx", col_meta_only=True)
my_col_metadata[0:5] # tested with siRNA file because of the file size

# AttributeError: module 'numpy' has no attribute 'typeDict'

Environment

songsong0425 commented 12 months ago

I solved this problem by downgrading numpy to 1.21.0. However, it will be better to upgrade cmapPy to use a higher version of numpy because of the dependency. I hope this problem is resolved quickly.