acdpretty

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Function

Description

acdpretty will generate a correctly, fully formatted ACD file from one which is parsable but which is partly or incorrectly formatted.

acdpretty reads the ACD file and rewrites it with clean formatting to the file (ApplicationName).acdpretty which can be used to overwrite the original ACD file. The new file might contain many differences. For example, abbreviations will be expanded, all sections and attributes will be indented, all values will be quoted and lines will be wrapped at a reasonable width.

Usage

% acdpretty qatest 

Created qatest.acdpretty

Go to the output files for this example

Command line arguments

All other command line parameters and qualifiers are essentially ignored as processing stops once the ACD file is printed. A few of the general qualifiers have the potential to conflict with the function of acdpretty.

Correctly reformat an application ACD file
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Input file format

Output file format

The output file is a pretty printed copy of the original ACD file.

All sections and attributed will be indented. All values will be quoted. Lines will be wrapped at a reasonable width.

The output file is intended as a standard format for parsers used by GUI and other interface wrappers, rather than using the original ACD file directly.

Output files for usage example

File: qatest.acdpretty

# Example ACD file for QA testing
#

application: qatest [
  groups: "test"
  documentation: "ACD file for QA testing"
]

sequence: asequence [
  parameter: "Y"
  features: "Y"
]

sequence: bsequence [
  parameter: "Y"
]

outfile: outfile [
  parameter: "Y"
]

integer: aint [
  prompt: "first integer"
]

integer: bint [
  prompt: "second integer, first was $(aint)"
  default: "57"
]

string: testalen [
  standard: "Y"
  information: "asequence length $(asequence.length)"
]

string: testblen [
  standard: "Y"
  information: "bsequence length $(bsequence.length)"
]

string: outdir [
  information: "output directory"
]

boolean: logic [
  information: "boolean value"
]

outfile: outtest [
  parameter: "Y"
  odirectory: "$(outdir)"
]

seqout: outseq [
  parameter: "Y"
  features: "Y"
  osdirectory: "$(outdir)"
  ofdirectory: "$(outdir)"
]

Data files

Notes

acdpretty does not have its own options, but takes a single parameter which is the name of the ACD file that is being processed. It is invoked by specifying the name of the ACD file after the name of the utility application itself:

acdpretty ApplicationName

Any command line parameters that would normally be specified for the application are essentially ignored as processing stops once the reformatted ACD file is printed.

The format generated by acdpretty is intended as a standard for parsers used by GUI and other interface developers. It is far easier writing a parser to cope with acdpretty output than one which can cope with the ACD sytax in general.

References

Warnings

A few of the global qualifiers have the potential to conflict with the function of acdpretty.

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

Comments