diff options
| author | BonfaceKilz | 2021-04-30 12:45:59 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-04-30 13:45:15 +0300 |
| commit | 03b6bcee689c1910bd850c6109cc37adc509cf5a (patch) | |
| tree | 2ca686d7f1b6649bfbd593607aa406eff8efbfb7 /wqflask/utility/gen_geno_ob.py | |
| parent | 6be1111fd76a2c47de7a20cc18bb9f4d8d2d4ffa (diff) | |
| download | genenetwork2-03b6bcee689c1910bd850c6109cc37adc509cf5a.tar.gz | |
autopep8: Fix E501
Diffstat (limited to 'wqflask/utility/gen_geno_ob.py')
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 12 |
1 files changed, 8 insertions, 4 deletions
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 24604e58..e619b7b6 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -38,13 +38,15 @@ class genotype: def read_rdata_output(self, qtl_results): # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results - self.chromosomes = [] # ZS: Overwriting since the .geno file's contents are just placeholders + # ZS: Overwriting since the .geno file's contents are just placeholders + self.chromosomes = [] this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for marker in qtl_results: locus = Locus(self) - if (str(marker['chr']) != this_chr) and this_chr != "X": # ZS: This is really awkward but works as a temporary fix + # ZS: This is really awkward but works as a temporary fix + if (str(marker['chr']) != this_chr) and this_chr != "X": if this_chr != "": self.chromosomes.append(chr_ob) this_chr = str(marker['chr']) @@ -156,9 +158,11 @@ class Locus: try: self.cM = float(marker_row[geno_ob.cm_column]) except: - self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 + self.cM = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 try: - self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + self.Mb = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None except: self.Mb = self.cM |