Update Databases.md

Update ink to extract usage on db page

Author: kelwyres

docs/Databases.md

@@ -427,7 +427,7 @@ database</td>
 </tbody>
 </table>
 
-<a id="kaptive-extract"></a>
+
 
 ## Extract
 
@@ -439,66 +439,4 @@ formats:
 - **ffn**: Gene nucleotide sequences in fasta format.
 - **faa**: Protein sequences in fasta format.
 
-### Usage
-
-General usage is as follows:
-
-    kaptive extract <db> [formats] [options]
-
-Formats:
-
-    Note, text outputs accept '-' for stdout
-
-    --fna []         Convert to locus nucleotide sequences in fasta format
-                     Accepts a single file or a directory (default: cwd)
-    --ffn []         Convert to locus gene nucleotide sequences in fasta format
-                     Accepts a single file or a directory (default: cwd)
-    --faa []         Convert to locus gene protein sequences in fasta format
-                     Accepts a single file or a directory (default: cwd)
-
-<a id="database-options"></a>
-
-Database options:
-
-    --locus-regex    Python regular-expression to match locus names in db source note
-    --type-regex     Python regular-expression to match locus types in db source note
-    --filter         Python regular-expression to select loci to include in the database
-
-!!! note
-    These options are useful for customising the database to your needs,
-    for example, to include only a subset of loci or to change the way
-    locus names and types are parsed from the source note.
-
-
-Other options:
-
-    -V, --verbose    Print debug messages to stderr
-    -v , --version   Show version number and exit
-    -h , --help      Show this help message and exit
-
-For example, to extract the gene nucleotide sequences from the
-*Klebsiella pneumoniae* K locus primary reference database in fasta
-format, run:
-
-    kaptive extract kp_k --fna k_loci.fna
-
-To extract all protein sequences from KL1 and KL2, run either one of the
-following:
-
-    kaptive extract kp_k --filter "^KL(1|2)$" --faa KL1_KL2_proteins.faa
-    kaptive extract kp_k --filter "^KL(1|2)$" --faa - > KL1_KL2_proteins.faa
-
-To do the same but output each locus to a separate file, run either:
-
-    kaptive extract kp_k --filter "^KL(1|2)$" --faa
-    kaptive extract kp_k --filter "^KL(1|2)$" --faa protein_files/
-
-Which would create two files: `KL1.faa` and `KL2.faa`.
-
-> kaptive assembly kpsc_k assembly.fasta -j kaptive_results.json
-
-!!! warning
-    It is possible to write **all** text formats (`fna`, `faa` and `ffn`)
-    to the same file (including stdout), however this is not recommended
-    for downstream analysis.
-
+See [here](Usage.md#kaptive-extract) for usage instructions.