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Diffstat (limited to 'Code/geneid2name.py')
-rw-r--r-- | Code/geneid2name.py | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/Code/geneid2name.py b/Code/geneid2name.py new file mode 100644 index 0000000..6d412f8 --- /dev/null +++ b/Code/geneid2name.py @@ -0,0 +1,29 @@ +# Purpose: refactoring. +# Create on 10 Aug 2019 by Hui Lan <lanhui@zjnu.edu.cn> + +def make_gene_name_AGI_map_dict(fname): + ''' + A dictionary that maps gene id to gene name, and gene name to gene id. + fname is ../Data/information/AGI-to-gene-names_v2.txt + ''' + d = {} + f = open(fname) + for line in f: + line = line.strip() + lst = line.split() + agi = lst[0].upper() + name_string = lst[1].upper() + d[agi] = name_string + for name in name_string.split(';'): + if not name in d: + d[name] = agi + f.close() + return d + + +def get_gene_name(gene_id, agi2name_dict): + if gene_id in agi2name_dict and agi2name_dict[gene_id] != gene_id: + gene_name = agi2name_dict[gene_id] + else: + gene_name = '.' + return gene_name |