[Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

[Shamshad A. <sha...@gm...>]

Hi,

I am working on Command Line Interface (CLI) which is a GSoC-2014 project.
And I would like get some  feedback on the commands and parameters used
with commands in CLI.

In the first phase, our aim is to implement the commands to generate
Scaffold tree from the molecules in the SDF file or in the database. We are
also offering user to specify the ring size of the scaffolds which are to
be included in output. The generated scaffold is saved in the sdf file that
can be further used for analysis. An SDF file is required to generate
scaffold tree from the file and connection data is needed to make
connection with database to generate scaffold tree from database.

In the later stages we have planned to implement filtering by structure and
substructure e. g. only certain subtrees based on the structure /
substructure search will saved in output.

These are proposed commands and their parameters so far:

(1) generate : This command is used to generate scaffold tree / network and
it needs a source of molecules like sdf file and a destination file to save
generated scaffolds. It is used in combination with following parameters -
(a) To generate scaffold tree / network loading molecules from file
-n | --network : Use this parameter to generate scaffold network, absence
of this parameter means you want to generate scaffold tree
-i | --input-file <file_location> : Specify location of input file to read
molecules from.
-o | --output-file <file_location> : Specify file in which generated
scaffold would be saved
-m | --max-ring-size <number> : Specify the maximum ring size of scaffold
that should be included in the output

(b) To generate scaffold tree / network by loading molecules from Scaffold
Hunter database
-c | --connection-name <connection-name> : Name of the connection that
would be used for connection with the database to retrieve molecules.
-d |  --dataset <dataset_name> : Specify name of the dataset to retrieve
molecules from and generate scaffold tree
-o | --output-file <file_location> : Specify file in which generated
scaffold would be saved
-m | --max-ring-size <number> : Specify the maximum ring size of scaffold
that should be included in the output
-n | --network : Use this parameter to generate scaffold network, absence
of this parameter means you want to generate scaffold tree

These are some examples of 'generate' command :

(a) Read molecules from file

sh generate -i <input-file>
Read molecules from input file and generate scaffold tree. Generated tree
is saved in a file automatically.

sh generate -i <input-file> -o scaffold.sdf
Read molecules from input file and generate scaffold tree. Generated tree
is saved in scaffold.sdf.

sh generate -i <input-file> -o scaffold-2.sdf -n
Read molecules from input file and generate scaffold 'network'. Generated
network is saved in scaffold-2.sdf.

sh generate -i <input-file> -o scaffold-3.sdf -m 5
Read molecules from input file and generate scaffold tree. Generated tree
is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are not
saved.

(b) Read molecules from database

sh generate -c <connection-name>
Read molecules from database which connection data is pointed by
<connection-name> and generate scaffold tree. Generated tree is saved in
file automatically.

sh generate -c <connection-name> -o scaffold.sdf
Read molecules from database which connection data is pointed by
<connection-name> and generate scaffold tree. Generated tree is saved in
scaffold.sdf.

Similarly, you can use -n to generate network and -m <number> to limit the
ring size as you've done in scaffold tree generation from file.

(2) connection [list | save | delete] : This command is used to manage
connection data which is required for connection with database. It is
followed by list, save or delete action. These are parameters supported by
the command :

-c | --connection-name <name> : name of the connection
-t | --database-type : Type of database (mySql, HSQLDB)
-u | --url : Url of the mySql database server or file location of HSQLDB
-n | --database-name : Name of the database
-un | --user-name : user name to login
-p | --password : password of the database (You can avoid this parameter
and specify it at runtime during connection is made to database)

Here is some uses of connection command -

sh connection list
display the names of available connections on screen

sh connection list -c <name>
display the details of particular connection data pointed by name excluding
password

sh connection delete -c <name>
delete the connection data pointed by the name

connection save -c <name> -t <hsqldb | mysql> -u <url> -n <database-name>
-un <user-name>
save a new connection data with specified name which can be used later to
make connection with database

Feedback -

We are seeking your feedback on implemented commands and proposed
parameters to make the command line interface more useful. So, please give
your inputs to a few questions given here :
1. What are the features of scaffold hunter you want to use in command line
interface?
2. Do you find the parameters provided for scaffold tree / network
generation user friendly?
3. Do you need some more parameters to control the generation strategy?
4. Do you think some proposed parameters are redundant? If so, please
specify the name of those parameters.

You may also put any other suggestions regarding command line interface

Thanks,
Shamshad

-- 
-Shamshad Alam

+91 9911631198 | India