Common Options to Command Line Programs

The PATRIC scripts accept a large number of options to control their action. There are a number of options that are common to many scripts. We describe these options here.

Input Options

The following option can be used to change where the input for the script is taken.

--input

Name of the main input file. If omitted and an input file is required, the standard input is used.

Column Options

The following options can be used to specify the column used for input data processing:

--col

Index (1-based) of the column number to contain the key field. If a non-numeric value is specified, it is presumed to be the value of the header in the desired column. This option is only present if the $colFlag parameter is TRUE. The default is 0, which indicates the last column.

--batchSize

Maximum number of lines to read in a batch. The default is 100. This option is only present if the $colFlag parameter is TRUE.

--nohead

Input file has no headers.

Data Options

The following options can be used to specify data to be retrieved from lookup routines.

--attr

Names of the fields to return. Multiple field names may be specified by coding the option multiple times or separating the field names with commas. Mutually exclusive with –count.

--count

If specified, a count of records found will be returned instead of the records themselves. Mutually exclusive with –attr.

--equal

Equality constraints of the form field-name,value. If the field is numeric, the constraint will be an exact match. If the field is a string, the constraint will be a substring match. An asterisk in string values is interpreted as a wild card. Multiple equality constraints may be specified by coding the option multiple times.

--lt

--le

--gt

--ge

--ne

Inequality constraints of the form field-name,value. Multiple constrains of each type may be specified by coding the option multiple times.

--in

Multi-valued equality constraints of the form field-name,value1,value2,…,valueN. The constraint is satisfied if the field value matches any one of the specified constraint values. Multiple constraints may be specified by coding the option multiple times.

--required

Specifies the name of a field that must have a value for the record to be included in the output. Multiple fields may be specified by coding the option multiple times.

Delimiter Options

The following option may be use to affect the delimiter used in writing output columns.

--delim

The delimiter to use between object names. The default is ::. Specify tab for tab-delimited output, space for space-delimited output, semi for a semicolon followed by a space, or comma for comma-delimited output. Other values might have unexpected results.