|   | prosextract | 
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prosextract processes the PROSITE motif database for use by patmatmotifs. It reads the prosite.dat and prosite.doc files (from the Prosite distribution) from the specified directory and writes an output file (by default called prosite.lines) with the following information (corresponding lines from prosite.dat given in parentheses): i. Identity (ID). ii. Accession number (AC). iii. Motif pattern (PA). iv. The motif pattern converted a regular expression. Additionally, one output file per accession number is written containing documentation from prosite.doc.
| % prosextract Process the PROSITE motif database for use by patmatmotifs PROSITE database directory [.]: | 
Go to the output files for this example
The output files named after the prosite accession numbers can now also be seen in the prosite directory. This files are automatically created after prosextract is run.
| 
Process the PROSITE motif database for use by patmatmotifs
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-prositedir]        directory  PROSITE database directory
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-prositedir" associated qualifiers
   -extension1         string     Default file extension
   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
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-prositedir] (Parameter 1) | directory | PROSITE database directory | Directory | |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-prositedir" associated directory qualifiers | ||||
| -extension1 -extension_prositedir | string | Default file extension | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
This directory contains output files.
This program most be run as a prerequisite to using patmatmotifs.
| Program name | Description | 
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX | 
| cutgextract | Extract codon usage tables from CUTG database | 
| jaspextract | Extract data from JASPAR | 
| printsextract | Extract data from PRINTS database for use by pscan | 
| rebaseextract | Process the REBASE database for use by restriction enzyme applications | 
| tfextract | Process TRANSFAC transcription factor database for use by tfscan | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.