# External annotation databases

## Import GENCODE human release 32

Next, we can annotate the genes in our GTEx expression dataset with genomics annotation from GENCODE. In this example,

we use the URL path prefix "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/" which specifies the

species and release version. We also pass a dictionary `file_resources`, with key-value pairs where the key is name of

file and value is the suffix of the file download URL.

For example, file_resources={"long_noncoding_RNAs.gtf": "gencode.v32.long_noncoding_RNAs.gtf.gz"} will download file

located at <ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.long_noncoding_RNAs.gtf.gz>

to process the `long_noncoding_RNAs.gtf` file.

Here, we loads both "long_noncoding_RNAs.gtf" and "basic.annotation.gtf" which builds a dataframe of combined

annotations for both lncRNAs and mRNAs. You can specify different annotation files options from GENCODE by modifying

the `file_resources` dict argument.

```{code-block} python

from openomics.database import GENCODE, EnsemblGenes

gencode = GENCODE(path="ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/",

                 file_resources={"long_noncoding_RNAs.gtf": "gencode.v32.long_noncoding_RNAs.gtf.gz",

                                 "basic.annotation.gtf": "gencode.v32.basic.annotation.gtf.gz",

                                 "lncRNA_transcripts.fa": "gencode.v32.lncRNA_transcripts.fa.gz",

                                 "transcripts.fa": "gencode.v32.transcripts.fa.gz"},

                 remove_version_num=True)

# We also loads Ensembl genes to get list of miRNA gene IDs

ensembl = EnsemblGenes(biomart='hsapiens_gene_ensembl', npartitions=8, )

```

## Setting the cache download directory

The package `astropy` is used to automatically cache downloaded files. It defaults to saving the files at

`~/.astropy/cache/`, where the cached content is retrieved given the matching URL. To change the path for the cache download file, run:

```python

import openomics

openomics.set_cache_dir(path="PATH/OF/YOUR/CHOICE/")

```

```{note}

Note that this setting doesn't persist across different programming sessions. Ideally, the cache dir should be in one location to minimize automatic FTP downloads, which may cause unnecessary stress on the database server.

```