search

biocore-ntnu / snpflip

Report reverse and ambiguous strand SNPs in GWAS data
33 stars 8 forks source link

snpflip issues #2

Closed DM2016 closed 7 years ago

DM2016 commented 7 years ago

Hello, I am having a problem with the snpflip code. When I run it, I use the following command:

snpflip --bim-file=CGEMS_LC_HumanHap550_FW_sample_level_c2_All_final.bim --fasta-genome=HG19.genome.fa

However, I'm getting the following error:

Traceback (most recent call last): File "/home/diego/Functions/GSE47718practice/SRPfiles/sratoolkit.2.5.1-centos_linux64/bin/snpflip", line 40, in from snp_flip.table import create_snp_table, find_strand ImportError: No module named snp_flip.table

I'm looking for this module and can't find it. Can anyone please help me with this error? Best, DM

endrebak commented 7 years ago

here it is: https://github.com/biocore-ntnu/snpflip/blob/master/snp_flip/table.py

How did you install the software? Pip install snpflip?

On Thursday, July 6, 2017, DM2016 notifications@github.com wrote:

Hello, I am having a problem with the snpflip code. When I run it, I use the following command:

snpflip --bim-file=CGEMS_LC_HumanHap550_FW_sample_level_c2_All_final.bim --fasta-genome=HG19.genome.fa

However, I'm getting the following error:

Traceback (most recent call last): File "/home/diego/Functions/GSE47718practice/SRPfiles/ sratoolkit.2.5.1-centos_linux64/bin/snpflip", line 40, in from snp_flip.table import create_snp_table, find_strand ImportError: No module named snp_flip.table

I'm looking for this module and can't find it. Can anyone please help me with this error? Best, DM

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore-ntnu/snpflip/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0rtGuw6sekk4toD_zV4KOpRUgDeAks5sLPyvgaJpZM4OPzLG .

endrebak commented 7 years ago

I'll take it that pip install snpflip worked then.