diff options
| -rw-r--r-- | wqflask/maintenance/dataset/genotypes.py | 23 |
1 files changed, 23 insertions, 0 deletions
diff --git a/wqflask/maintenance/dataset/genotypes.py b/wqflask/maintenance/dataset/genotypes.py index c83fb8b7..164f0ff6 100644 --- a/wqflask/maintenance/dataset/genotypes.py +++ b/wqflask/maintenance/dataset/genotypes.py @@ -11,3 +11,26 @@ def get_geno(inbredsetid, name): """ cursor.execute(sql, (inbredsetid, name)) return cursor.fetchone() + +def load_genos(file): + genotypes = [] + file_geno = open(file, 'r') + for line in file_geno: + line = line.strip() + if line.startswith('#'): + continue + if line.startswith('@'): + continue + cells = line.split() + if line.startswith("Chr"): + strains = cells[4:] + continue + genotype = {} + genotype['chr'] = cells[0] + genotype['locus'] = cells[1] + genotype['cm'] = cells[2] + genotype['mb'] = cells[3] + genotype['values'] = cells[4:] + genotypes.append(genotype) + return strains, genotypes +
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