AttributeError: TranscriptionMatrix instance has no attribute 'gene_list'
julandalf opened this issue · 3 comments
./PrediXcan.py --predict --assoc --linear
--weights weights/Brain_Frontal_Cortex_BA9/gtex_v7_Brain_Frontal_Cortex_BA9_imputed_europeans_tw_0.5_signif.db
--dosages genotype/
--dosages_prefix "chr22.dosage.txt.gz"
--samples genotype/chr22.txt
--pheno phenotype/phenotype.txt
--output_prefix results/chr22
2018-05-03 15:28:56.746566 Preloading weights...
2018-05-03 15:28:56.970715 Processing chr22.dosage.txt.gz
Traceback (most recent call last):
File "./PrediXcan.py", line 230, in
main()
File "./PrediXcan.py", line 212, in main
transcription_matrix.save(PRED_EXP_FILE)
File "./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'
Hello julandalf,
Could you please confirm that your dosage file complies with the format:
chromosome rsid position allele1 allele2 MAF id1 ..... idn
?
Notice that the second column must contain rsid's for the SNPs (and not other kind of ID's, like chr:position
). This is important because this is the way the SNPs in your dosage files are matched with the SNPs in the prediction models.
If all of this looks good, I will ask you some other questions to figure out what the problem is.
Thanks,
Rodrigo
Hello,
Could you solve your problem? If so, I would like to close this issue.
Thanks,
Rodrigo
Closing for lack of activity.