Hello,
I would like to know how can I obtain coordinates from one assembly to another, say GRCh38 to GRCh37, using MySQL connection to ensembldb.ensembl.org
?
I know ensembl has a REST API (http://rest.ensembl.org
) that can be used to question the database but I am looking for a direct connection that could ease the implementation into my workflow using a single query (instead of a script with API).
See this example for the REST API: http://rest.ensembl.org/map/human/GRCh38/1:942451..942451:1/GRCh37?
The coordinates of the chromosome 1 on 942,451 are converted to GRCh37.
I would like to do similarly but using a MySQL query.
For example, I have a file containing the following coordinates in GRCh38:
#chrom GRCh38_pos
1 69511
1 930314
1 942451
1 953279
1 953778
I expect to get a file containing the following:
#chrom GRCh38_pos GRCh37_pos
1 69511 69511
1 930314 865694
1 942451 877831
1 953279 888659
1 953778 889158
How can I do this using MySQL query connection to ensembldb ?
PS: to connect to MySQL ensembl:
mysql -u anonymous --host=ensembldb.ensembl.org
or
mysql -A -u anonymous --host=ensembldb.ensembl.org
to turn off completion of table and column names.
Thank you.
Hello Pierre,
Could I ask why not ? Isn't ensembl REST API based on ensembl MySQL ? If yes, shouldn't it then be possible ?
because not everything is computed in mysql.