| ## EMBOSS: swissparse

# Program swissparse

## Function

Retrieves sequences from swissprot using keyword search

## Description

**************** EDIT HERE ****************

## Usage

Here is a sample session with swissparse:

    % swissparse

**************** EDIT HERE ****************

## Command line arguments

       Mandatory qualifiers:
      [-keyfile]           infile     Name of keywords file for input
      [-spfile]            infile     Name of swissprot database to read
      [-outfile]           outfile    Name of search results file for output

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-keyfile] (Parameter 1) | Name of keywords file for input | Input file | scop.terms
[-spfile] (Parameter 2) | Name of swissprot database to read | Input file | ./seq.dat
[-outfile] (Parameter 3) | Name of search results file for output | Output file | scop.seqs
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

**************** EDIT HERE ****************

## Output file format

**************** EDIT HERE ****************

## Data files

**************** EDIT HERE ****************

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
coderet | Extract CDS, mRNA and translations from feature tables
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
showfeat | Show features of a sequence
splitter | Split a sequence into (overlapping) smaller sequences
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk) **************** EDIT HERE ****************

## History

Written (date) - author. **************** EDIT HERE ****************

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments