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Diffstat (limited to 'gn3/computations/rqtl.py')
| -rw-r--r-- | gn3/computations/rqtl.py | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index 21c863a..9c1c7cd 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -312,16 +312,16 @@ def process_perm_output(file_name: str) -> Tuple[List, float, float]: suggestive and significant thresholds""" perm_results = [] - outdir = os.path.join(get_tmpdir(),"gn3") + outdir = os.path.join(get_tmpdir(), "gn3") - with open( os.path.join(outdir,file_name),"r",encoding="utf-8") as the_file: + with open(os.path.join(outdir, file_name), "r", encoding="utf-8") as the_file: for i, line in enumerate(the_file): if i == 0: # Skip header line continue - line_items = line.split(",") - perm_results.append(float(line_items[1].replace("\"", ""))) + snp, chromosome, position, lod_score = line.split(",") + perm_results.append(float(lod_score)) suggestive = np.percentile(np.array(perm_results), 67) significant = np.percentile(np.array(perm_results), 95) |