Design proposal...

Add a method Ag3.sample_cohorts(sample_sets, analysis):

The sample_sets parameter is string or list, default to "v3_wild", same as for other methods like sample_metadata().
The analysis parameter is a string with default value set to latest analysis.
Return value is a pandas dataframe with columns sample_id, admin1_year, admin1_month, admin2_year, admin2_month.

This method basically just reads the CSV files created by the cohorts analysis, and concatenates for multiple sample sets if requested.

Example:

df_cohorts = ag3.sample_cohorts(sample_sets="v3_wild")

Moved to #57

Modify method Ag3.snp_allele_frequencies(transcript, cohorts, cohorts_analysis, ...):

Allow the cohorts parameter to be a dict (current behaviour continues to be supported) or a string. If a string, it must be the name of one of the columns in the cohorts dataframe.
Add a cohorts_analysis parameter which is a string with default value set to latest cohorts analysis. This will be used if the cohorts parameter is given as a string.
Other parameters left as-is.

Open questions:

Example:

df_snp_af = ag3.snp_allele_frequencies(transcript="AGAP006028-RA", cohorts="admin1_month")

Moved to #59

Modify method Ag3.gene_cnv_frequencies(contig, cohorts, cohorts_analysis, ...):

Allow the cohorts parameter to be a dict (current behaviour continues to be supported) or a string. If a string, it must be the name of one of the columns in the cohorts dataframe.
Add a cohorts_analysis parameter which is a string with default value set to latest cohorts analysis. This will be used if the cohorts parameter is given as a string.
Other parameters left as-is.

Open questions:

Example:

df_cnv_gene = ag3.gene_cnv_frequencies(contig="2R", cohorts="admin1_month")

cc @cclarkson -- thinking ahead here to how the cohorts will be used.

Add access to predefined cohorts #51

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