EMBOSS: acdlog

| acdlog

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Test application ACD file processing and trace data structures

## Description

acdlog processes an ACD file and user input, while logging the contents of internal data structures. For the time being it's use is deprecated and the entrails application should be used instead.

acdlog works the same as acdc but reports on the data structures used to process the ACD file.

## Usage

Here is a sample session with acdlog

    % acdlog antigenic
    Finds antigenic sites in proteins
    Input protein sequence(s): tsw:actb1_takru
    Minimum length of antigenic region [6]:
    Output report [actb1_takru.antigenic]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

The first parameter is the name of the program to compile. All other command line parameters and qualifiers are defined for that program - see the documentation for the program of choice.

## Output file format

The output file of the program being logged is empty, but any format available to the specified program can be used.

The processing output is written to a file with the extension ".acdlog"

### Output files for usage example

### File: actb1_takru.antigenic

### File: antigenic.acdlog

    testing acdpromptsacdArgsScan acdDebug No acdDoHelp No
    Trying acdfile '/homes/pmr/local/share/EMBOSS/acd/antigenic.acd' (installed)
    Code file installed: '/homes/pmr/local/share/EMBOSS/acd/codes.english'
    Code file /homes/pmr/local/share/EMBOSS/acd/codes.english used
    add to table defalign 'Write output alignment to'
    add to table defreport 'Write output report to'
    add to table definteger 'Enter a number'
    add to table deffloat 'Enter a number'
    add to table defbool 'Yes or No'
    add to table defdirectory 'Which directory'
    add to table defoutfile 'Write output to'
    add to table deffeatout 'Write features  to'
    add to table defseqout 'Write sequence to'
    add to table defseqoutset 'Write sequence set to'
    add to table defseqoutall 'Write sequences to'
    add to table defsequence 'Read sequence from'
    add to table defseqset 'Read sequence set from'
    add to table defseqall 'Read sequences from'
    add to table defstring 'Enter text'
    add to table defgraph 'Graph type'
    add to table defxygraph 'Graph type'
    add to table defrange 'Range(s)'
    add to table helpdirectory 'Directory name'
    add to table helpoutfile 'Output file name'
    add to table helpalign 'Output alignment file name'
    add to table helpreport 'Output report file name'
    add to table helpfeatout 'Output features UFO'
    add to table helpseqout 'Output sequence USA'
    add to table helpseqoutset 'Output sequence set USA'
    add to table helpseqoutall 'Output sequence(s) USA'
    add to table helpsequence 'Sequence USA'
    add to table helpseqset 'Sequence set USA'
    add to table helpseqall 'Sequence database USA'
    add to table helpgraph 'Graph type'
    add to table helpxygraph 'Graph type'
    add to table helpcodon 'Codon usage table name'
    add to table helpoutcodon 'Codon usage table name'
    add to table helpobo 'Ontology term query'
    add to table helpoutobo 'Output ontology term file name'
    add to table helpresource 'Data resource catalogue query'
    add to table helpoutresource 'Output data resource file name'
    add to table gap 'What gap penalty'
    add to table gapext 'What gap extension penalty'
    add to table fred 'Sanger special'
    add to table ciao 'Hello from Bari'
    Knowntypes file installed: '/homes/pmr/local/share/EMBOSS/acd/knowntypes.standard'
    Knowntypes file /homes/pmr/local/share/EMBOSS/acd/knowntypes.standard used
    acdSetDefC auto 'N' 1202710
    acdSetDefC stdout 'N' 11eb970
    acdSetDefC filter 'N' 11ebba0

      [Part of this file has been deleted for brevity]

          Assoc: No
     AssocQuals: rformat
        Defined: No
        Userdefined: No
    Orig. Value: ''
          Value: 'actb1_takru.antigenic'

          Default Attributes:
             default: 'actb1_takru.antigenic'
         information: ''
              prompt: ''
                code: ''
                help: ''
           parameter: 'Y'
            standard: 'Y'
          additional: ''
             missing: ''
               valid: ''
            expected: ''
              needed: ''
           knowntype: ''
           relations: 'EDAM:0001534 data Peptide immunogenicity report'
      outputmodifier: ''
               style: ''
           qualifier: ''
            template: ''

          Attributes:
                type: ''
             taglist: 'int:pos=Max_score_pos'
            multiple: 'Y'
           precision: ''
         nulldefault: ''
              nullok: ''

    ACD 48
           Name: 'output'
          Token: 'output'
          Param: 0
          Level: 6   (ENDSEC)
       Key Type: 5   (endsection)
          NAttr: 0
          Assoc: No
     AssocQuals: <undefined>
        Defined: No
        Userdefined: No
    Orig. Value: '<null>'
          Value: <undefined>

          Attributes:

## Data files

Acdlog will use any data files specified in the ACD file of the specified program, but will ignore any data files that are only used directly by the program's code.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

acdlog does not have its own options, but takes a single parameter which is the name of the EMBOSS application that is being testsed. It is invoked by specifying the name of the application to be tested along with any command-line options after the name of the utility application itself:

`acdlog ApplicationName Options`

acdlog will run the command line interface of any EMBOSS program by reading its ACD file and processing the command line and user responses in exactly the same way as if the true program itself were running. The application proper is not run; it is only the ACD file that is read. Any command-line options for the application being called can be specified. The user is prompted for any required values for application parameters and any input files are read. Output files can be specified in any available format however they will be empty (the application code is not called so there will be no output).

## References

## Warnings

None.

## Diagnostic Error Messages

## Exit status

It exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
acdc | Test an application ACD file
acdpretty | Correctly reformat an application ACD file
acdrelations | Add relations: attribute to ACD files
acdtable | Generate an HTML table of parameters from an application ACD file
acdtrace | Trace processing of an application ACD file (for testing)
acdvalid | Validate an application ACD file

## Author(s)

Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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

## History

## Target users

This program is intended to be used by developers of applications and interfaces.

## Comments

None