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 Processes 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.
Processes the PROSITE motif database for use by patmatmotifs Version: EMBOSS:6.4.0.0 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.