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| author | zsloan | 2019-10-08 14:28:42 -0500 |
|---|---|---|
| committer | zsloan | 2019-10-08 14:28:42 -0500 |
| commit | bd13472a05b947b809a8199584d6a3cf5dfad703 (patch) | |
| tree | 59433860eaca80b10185fa73f4783fb8974d7844 /wqflask/utility | |
| parent | 5cffa1eacdb7fbb3d65b49744b0bee43e4cb130d (diff) | |
| download | genenetwork2-bd13472a05b947b809a8199584d6a3cf5dfad703.tar.gz | |
Fixed serious issue that caused output to be wrong for new reaper mapping
Haplotype analyst now works for GEMMA
Increased margin a bit to fix minor issue with buttons getting cut off on certain Safari versions for bar chart
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 15 |
1 files changed, 8 insertions, 7 deletions
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index e8780879..44e2722f 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -47,20 +47,20 @@ class genotype(object): elif line[0] == "@": label = line.split(":")[0][1:] if label == "name": - self.group = line.split(":")[1] + self.group = line.split(":")[1].strip() elif label == "filler": - if line.split(":")[1] == "yes": + if line.split(":")[1].strip() == "yes": self.filler = True elif label == "type": - self.type = line.split(":")[1] + self.type = line.split(":")[1].strip() elif label == "mat": - self.mat = line.split(":")[1] + self.mat = line.split(":")[1].strip() elif label == "pat": - self.pat = line.split(":")[1] + self.pat = line.split(":")[1].strip() elif label == "het": - self.het = line.split(":")[1] + self.het = line.split(":")[1].strip() elif label == "unk": - self.unk = line.split(":")[1] + self.unk = line.split(":")[1].strip() else: continue elif line[:3] == "Chr": @@ -133,6 +133,7 @@ class Locus(object): start_pos = 4 else: start_pos = 3 + for allele in marker_row[start_pos:]: if allele in geno_table.keys(): self.genotype.append(geno_table[allele]) |