Source Command

GORSQL¶

The GORSQL command allows you to run arbitrary SQL commands against “the database” (the database here being defined by the content of a file called gor.sql.credentials in the config directory).

For GORSQL to work properly, the defined query must return Chrom-POS information as first two columns.

SQL statements need to be encapsulated between curly brackets, e.g. gorsql {sql_query}.

Usage¶

gorsql <options> {<sql_query>} | ...

Options¶

`-p chr:pos1-pos2`	Choose a specific chromosome and position or a range to read. Both pos1 and pos2 are included. The following place holders are provided: #{CHROM}, #{BPSTART}, #{BPSTOP}.
`-f A[,B]*`	List of tags to filter files and file contents on. The following place holders are provided: #{TAGS}. The necessary quoting is done automatically.
`-ff File`	Read tags from a tag file and filter files and file contents on. Also accepts a nested query. The following place holders are provided: #{TAGS}. The necessary quoting is done automatically.
`-db database`	Database alias as defied in `gor.sql.credentials`.

Examples¶

gorsql {select Chrom, Pos, Reference, Call from GWAS_Subset WHERE Phenotype = 'Cancer' order by Chrom,Pos} | ...

gorsql -p chr3:1000- {select Chrom, Pos, Reference, Call from GWAS_Subset WHERE chrom = #{CHROM} and POS >= #{BPSTART} order by Chrom,Pos} | ...

gorsql -f AAA,TTT {select Chrom, Pos, Reference, Call from GWAS_Subset WHERE Call in (#{TAGS}) order by Chrom,Pos} | ...