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hakyim / TO-DELETE-PrediXcan

Code for the in-dev PrediXcan Project
MIT License
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AttributeError: TranscriptionMatrix instance has no attribute 'gene_list' #19

Closed Shenglai closed 7 years ago

Shenglai commented 7 years ago

Hi all,

I'm trying to run PrediXcan (master branch, commit 8bca77417e33b74d3233b1598969a953a882dc42)with 3615 TCGA samples on both TW_Lung_0.5.db and TW_Breast_Mammary_Tissue_0.5.db. However, I got an error saying 

  File "/mnt/SCRATCH/PrediXcan/Software/PrediXcan.py", line 214, in <module>
    main()
  File "/mnt/SCRATCH/PrediXcan/Software/PrediXcan.py", line 197, in main
    transcription_matrix.save(PRED_EXP_FILE)
  File "/mnt/SCRATCH/PrediXcan/Software/PrediXcan.py", line 117, in save
    outfile.write('FID\t' + 'IID\t' + '\t'.join(self.gene_list) + '\n') # Nb. this lists the names of rows, not of columns
AttributeError: TranscriptionMatrix instance has no attribute 'gene_list'

I've tried run PrediXcan with and without --genelist flag, but neither worked. The exact cmd I used is :

/path/to/PrediXcan.py --predict --dosages /path/to/dosage/ --dosages_prefix chr --samples tcga.impute2.fam --weights /path/to/TW_Breast_Mammary_Tissue_0.5.db --output_dir tcga_3615_brca_gtex_model (--genelist /path/to/gene_breast.txt) #The gene_breast.txt is actually #1 column from TW_Breast_Mammary_Tissue_0.5.txt

Please let me know if more information is required. Thank you so much!