No more non-unique column names, or non-queryable columns in list_columns

[ivirshup]

• Fixes list_columns includes columns from "metadata" and "chromosome" table #42

[gamazeps]

columns = [c for t in tables for c in self.db.table(t).columns]
return list(sorted(set(columns)))

is shorter and more readable no ?

It even works with the current tests

[ivirshup]

I think things are grouped a little more logically when it's ordered by table:

Example

In [2]: ensdb = gf.ensembl.annotation("Hsapiens", 108)

In [3]: ensdb.list_columns()
Out[3]: 
['gene_id',
 'gene_name',
 'gene_biotype',
 'gene_seq_start',
 'gene_seq_end',
 'seq_name',
 'seq_strand',
 'seq_coord_system',
 'description',
 'gene_id_version',
 'canonical_transcript',
 'tx_id',
 'tx_biotype',
 'tx_seq_start',
 'tx_seq_end',
 'tx_cds_seq_start',
 'tx_cds_seq_end',
 'tx_support_level',
 'tx_id_version',
 'gc_content',
 'tx_external_name',
 'tx_is_canonical',
 'exon_id',
 'exon_idx',
 'exon_seq_start',
 'exon_seq_end',
 'seq_length',
 'is_circular',
 'protein_id',
 'protein_sequence',
 'uniprot_id',
 'uniprot_db',
 'uniprot_mapping_type',
 'protein_domain_id',
 'protein_domain_source',
 'interpro_accession',
 'prot_dom_start',
 'prot_dom_end',
 'entrezid']

In [4]: sorted(ensdb.list_columns())
Out[4]: 
['canonical_transcript',
 'description',
 'entrezid',
 'exon_id',
 'exon_idx',
 'exon_seq_end',
 'exon_seq_start',
 'gc_content',
 'gene_biotype',
 'gene_id',
 'gene_id_version',
 'gene_name',
 'gene_seq_end',
 'gene_seq_start',
 'interpro_accession',
 'is_circular',
 'prot_dom_end',
 'prot_dom_start',
 'protein_domain_id',
 'protein_domain_source',
 'protein_id',
 'protein_sequence',
 'seq_coord_system',
 'seq_length',
 'seq_name',
 'seq_strand',
 'tx_biotype',
 'tx_cds_seq_end',
 'tx_cds_seq_start',
 'tx_external_name',
 'tx_id',
 'tx_id_version',
 'tx_is_canonical',
 'tx_seq_end',
 'tx_seq_start',
 'tx_support_level',
 'uniprot_db',
 'uniprot_id',
 'uniprot_mapping_type']

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.06%. Comparing base (bae82d2) to head (66c32d8).
Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #70      +/-   ##
==========================================
+ Coverage   92.94%   93.06%   +0.12%     
==========================================
  Files           6        6              
  Lines         340      346       +6     
==========================================
+ Hits          316      322       +6     
  Misses         24       24              

Files with missing lines	Coverage Δ
src/genomic_features/ensembl/ensembldb.py	93.10% <100.00%> (+0.21%)	⬆️