[docs]def gene_position(gff_file, get_dict=True):
"""Get the start and end position of each gene and determine their respective length.
Input is a .gff file downloaded from https://www.ensembl.org/Saccharomyces_cerevisiae/Info/Index
Output is a dictionary that includes all gene names as keys. The values are lists with four inputs.
The first is the chromosome number the gene belong to, the second is the start position, the third is the end position of the gene in terms of basepairs, the fourth is the reading orientation of the gene.
The reading orientation is indicated with a '+' (forward reading) or '-' (reverse reading).
The get_dict by default sets that the output should be given as a dictionary with keys the different genes and the values a list of the different parameters.
When the get_dict is set to False, the code returns all the values as individual lists.
Parameters
----------
gff_file : str
The file path of a .gff file downloaded from https://www.ensembl.org/Saccharomyces_cerevisiae/Info/Index
get_dict : bool, optional
When the get_dict is set to False, the code returns all the values as individual lists, by default True
Returns
-------
dict
Output is a dictionary that includes all gene names as keys. The values are lists with four inputs.
The first is the chromosome number the gene belong to, the second is the start position, the third is the end position of the gene in terms of basepairs, the fourth is the reading orientation of the gene.
The reading orientation is indicated with a '+' (forward reading) or '-' (reverse reading).
"""
if get_dict == True:
gene_pos_dict = {}
with open(gff_file) as f:
for line in f:
line_list = line.split("\t")
if len(line_list) > 2:
if line_list[2] == "gene":
gene_chr = line_list[0]
gene_start = line_list[3]
gene_end = line_list[4]
gene_orien = line_list[6]
gene_position = [
gene_chr,
int(gene_start),
int(gene_end),
gene_orien,
]
gene_name_string = line_list[8].split(";")[0]
gene_name = gene_name_string.split(":")[1]
gene_pos_dict[gene_name] = gene_position
return gene_pos_dict
else:
gene_chr = []
gene_start = []
gene_end = []
gene_orien = []
gene_name = []
with open(gff_file) as f:
for line in f:
line_list = line.split("\t")
if len(line_list) > 2:
if line_list[2] == "gene":
gene_chr.append(line_list[0])
gene_start.append(int(line_list[3]))
gene_end.append(int(line_list[4]))
gene_orien.append(line_list[6])
gene_name_string = line_list[8].split(";")[0]
gene_name.append(gene_name_string.split(":")[1])
return (gene_name, gene_chr, gene_start, gene_end, gene_orien)
