`transcripts`, `exons` functions + some filters

[ivirshup]

Fixes #12

transcripts + exons methods

TODO:

• [x] Tests
  • [x] Tests for exons are really slow when many results are returned. Should figure out if we can work around that.
• [x] Figure out what columns ensembldb returns by default, and copy what it does
  • ensembldb includes a tx_name field that seems to be the same as tx_id, which I am excluding

> colnames(tx@elementMetadata)
 [1] "tx_id"            "tx_biotype"       "tx_cds_seq_start" "tx_cds_seq_end"  
 [5] "gene_id"          "tx_support_level" "tx_id_version"    "gc_content"      
 [9] "tx_external_name" "tx_is_canonical"  "tx_name"  

Note: you can use an sqlite file with the R package via ensembldb::EnsDb("path/to/db.sqlite")

[codecov-commenter]

Codecov Report

Merging #44 (b783298) into main (67631b5) will decrease coverage by 3.51%. The diff coverage is 93.25%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #44 +/- ## ========================================== - Coverage 93.12% 89.61% -3.51% ========================================== Files 6 6 Lines 320 366 +46 ========================================== + Hits 298 328 +30 - Misses 22 38 +16 ``` | [Impacted Files](https://app.codecov.io/gh/scverse/genomic-features/pull/44?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | Coverage Δ | | |---|---|---| | [src/genomic\_features/filters.py](https://app.codecov.io/gh/scverse/genomic-features/pull/44?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvZmlsdGVycy5weQ==) | `100.00% <ø> (ø)` | | | [src/genomic\_features/\_core/filters.py](https://app.codecov.io/gh/scverse/genomic-features/pull/44?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvX2NvcmUvZmlsdGVycy5weQ==) | `84.24% <81.81%> (-8.91%)` | :arrow_down: | | [src/genomic\_features/ensembl/ensembldb.py](https://app.codecov.io/gh/scverse/genomic-features/pull/44?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvZW5zZW1ibC9lbnNlbWJsZGIucHk=) | `93.68% <97.01%> (+1.04%)` | :arrow_up: |

[lauradmartens]

Very nice rewrite of my join functions!! I don't have any objections except for the get_required_tables function.

[ivirshup]

Thanks! I mostly translated it from this code in ensembldb.

While I was adding the chromosome test:

• I made some of the exon tests faster by choosing filters with smaller results
• Realized we had different results from ensembldb, and added a distinct operation to fix that