gor query vs gor

[Shicheng-Guo]

Share 3 commands which I used to practice gor.

gor query /home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | head
gor query /home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10
gor /home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10

For the above 3 commands, only the first one works well and the following 2 don’t work. Do you have some comments or suggestion?

Here is the gor I used:

(base) [sguo2@comet-ln2 gor]$ gor
GOR Command Line

Usage:

gor [-v] [COMMAND]

Description:

Command line interface for gor query language and processes.

Options:

  -v, --version   Print version information and exits.

Commands:

  query, q    Execute a gor query, script or template
  help, h     Gives help on gor commands and functions.
  manager, m  Gor table manager operations.
  index, i    Index gor data files
  cache, c    Cache management
  render, r   Render reports and scripts
  info        List general gor information

(c) WuxiNextcode 2019

[gmagnu]

You need to put quotes ("") around your query, otherwise the | is interpreted by the shell and the command that follows is a shell command. The error message you are getting are from the shell that does not under stand the 'top' command. The first case works as head is a valid shell command. The second two cases should have been:

gor query "/home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10"
gor "/home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10"

Note: that if no command follows gor it defaults to query

The first use case shows how you can mix gor and shell commands.