Convert gene_IDs_names to toml

[manulera]

Create a script get_data/convert_genes2toml.py that writes the file data/genes.toml from data/gene_IDs_names.tsv, the same way that get_data/convert_alleles2toml.py writes data/alleles_pombemine.tsv.

What the fields are is explained in the readme.

For a row in the file, such as:

SPAC1250.01	snf21	SPAC29A4.21,brg1

The output should be

# Note that here the gene name is doublequoted, because it contains a dot, so that toml doesn't think we 
# are specifying a subclass. You don't have to specify this in python, you can use 'SPAC1250.01' as a dictionary
# key, and it will know to format it like this for the output.
[gene."SPAC1250.01"] 
ref = "SPAC1250.01"
# "name" will be empty sometimes. Not all genes have a preferred name.
# This should be taken into account when replacing gene names
name = "snf21"
# This field will be missing sometimes (not all genes have synonyms).
synonyms = ["SPAC29A4.21", "brg1"]

[manulera]

Hi @anamika-yadav99

I had a look at the first implementation. There are some issues with it, I have added some comments:

8af4e1e#r76881074

Some more details. If the gene has no synonyms (third column is empty), then it should not have the synonyms attribute in toml

[gene."SPNCRNA.4639"]
name = "SPNCRNA.4639" # name should not be added if 2nd column is empty
ref = "SPNCRNA.4639" # This should always be here
synonyms = [ "SPNCRNA.4639",] # synonyms should not be added if 3rf column is empty

[anamika-yadav99]

@manulera this issue is resolved I think. The final commit to solve this issue : 876c380

[manulera]

Good job @anamika-yadav99 ! The function does what it should do, just a few details on the code style:

genestorian_data_refinement/get_data/convert_gene2toml.py

Lines 15 to 16 in 42f3e07

	if len(ls) > 1:
	if ls[1] != '':

When checking two conditions, use and instead of two subsequent if statements. When you use and the first statement is checked first, so when you write if len(ls) > 1 and ls[1] != '': the second part of the statement is only executed if the first one is true, so even if the length of ls is only 1, ls[1] will not be executed and will not give an error. Same applies to line 19.

genestorian_data_refinement/get_data/convert_gene2toml.py

Line 21 in 42f3e07

synonyms = re.split(",", ls[2])

You don't need to use re here, regular string splitting should work. You can then remove the import of re module as well.

[manulera]

Added in #23