validate - validate and fix column values of a starbase data table

SYNOPSYS

        validate 'statements' < tablefile

validate executes a list of awk pattern statement pairs on each row of a starbase data table. Each statement is separated from the next by a semi-colon or newline. validate is very useful for checking and fixing values of columns in a table.

The statements or expression is preprocessed by the program before passed to awk for evaluation. Column and header value names are substituted for thier values in the table. Column names may be subscripted with an array index and the column data will be split on the ARRDEL environment variable. Header values may be also subscripted, but assignments made to header values will not appear in the output table.

The user statements and expressions of are interpreted by the awk programming langauge.

• A explaination of the available syntax in given in the mawk manual page.
• Extensions to awk implimented here at SAO and described on the tawk manual page.
• An introduction and reference manual for gawk is also available. There are some differences in implimentation between gawk and mawk but the manual provides an excellent reference.

• -i file Read input from file instead of the standard input.
• -o file Write output to file instead of the standard input.
• -D Print out the awk program to be executed before executing it.
• -H Specify an alternate file for the starbase data table header. When the -H option is given the input file should not have a header.

Check the rows of a table for consistancy. X must be less than 7 and Y must be less than 4.

    john@panic : validate 'X > 7 && Y < 4 { print "Warning bad position at line " NR }'

Validate programs can be quite complex and are very powerful. FastFixes used validate to check and fix the initial versions of the FAST database.

• TABLEAWK the name of the awk interpreter to execute. The default interpreter is tawk.
• TABLEFUNCTIONS a path specifying directories to find the source for undefined functions.

  Undefined user written function may be automatically included in the text of programs. The environment variable TABLEFUNCTIONS names a path which is searched for undefined functions. If a function is mentioned in a user program or expression but not defined, a file found in the TABLEFUNCTIONS path with the name of the undefined function will be included in the program. This feature allows a library of usefull functions to be built and accessed easily.

• ARRDEL array delimiter for splitting columns into arrays.

• calc - a command line calcutator
• row, select - select rows from a starbase table
• compute - compute column values for the rows of a starbase data table
• validate - conditionally run statements on the rows of a starbase data table
• reckon - evaluate awk statments as a user program.
• mawk an implementation of the awk programming language by Mike Brennan.
• tawk Awk language extensions implemented at SAO.

• starbase.1 starbase data table introduction.
• starbase.3 starbase data table C library.
• starbase.5 starbase data table file format.