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| author | Alexanderlacuna | 2020-11-09 13:20:53 +0300 |
|---|---|---|
| committer | Alexanderlacuna | 2020-11-09 13:20:53 +0300 |
| commit | 7aaa4b87fcf405c32c11e2e2d664941c43c14430 (patch) | |
| tree | 198a93a3bf5cb68f67e11cc74247c8743eb0842e /wqflask | |
| parent | 5e50e19a014efdfcf0ce1397025879d4ada4d271 (diff) | |
| download | genenetwork2-7aaa4b87fcf405c32c11e2e2d664941c43c14430.tar.gz | |
refactor marker_regression/gemma-mapping.py run-gemma function to avoid Index Error
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 9 |
1 files changed, 2 insertions, 7 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 68a8d5ba..02f91a32 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -31,16 +31,11 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) this_chromosomes = this_dataset.species.chromosomes.chromosomes - chr_list_string = "" - for i in range(len(this_chromosomes)): - if i < (len(this_chromosomes) - 1): - chr_list_string += this_chromosomes[i+1].name + "," - else: - chr_list_string += this_chromosomes[i+1].name + this_chromosomes_name=[chromosome.name for chromosome in this_chromosomes] + chr_list_string=",".join(this_chromosomes_name) if covariates != "": gen_covariates_file(this_dataset, covariates, samples) - if use_loco == "True": generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), genofile_name, |