AttributeError: TranscriptionMatrix instance has no attribute 'gene_list'

[julandalf]

./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'

[rbonazzola]

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

[rbonazzola]

Hello,

Could you solve your problem? If so, I would like to close this issue.

Thanks,
Rodrigo

[Heroico]

Closing for lack of activity.