EMBOSS: seqretset


Program seqretset

Function

Reads and writes (returns) a set of sequences all at once

Description

Usage

Here is a sample session with seqretset.

% seqretset
Reads and writes (returns) a set of sequences all at once
Input sequence set: embl:eclac*
Output sequence [outfile.fasta]: 

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqset     Sequence set USA
  [-outseq]            seqoutset  Output sequence set USA

   Optional qualifiers: (none)
   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence set USA Readable sequences Required
[-outseq]
(Parameter 2)
Output sequence set USA Writeable sequences <sequence>.format
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Output file format

The output from seqretset is a set of sequences, and by default will be written in FASTA format all in one file.

In some cases the output filename will be the same as the input filename, but as seqretset reads all the sequences before opening the output file it will safely overwrite. Note that this is not true of seqretall which only reads the first sequence before opening the ouput file, but is true of seqret which reads the first sequence at startup.

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
cirdnaDraws circular maps of DNA constructs
lindnaDraws linear maps of DNA constructs
remapDisplay a sequence with restriction cut sites, translation etc
seqretReads and writes (returns) sequences
seqretallReads and writes (returns) a set of sequences one at a time
seqretsplitReads and writes (returns) sequences
showfeatShow features of a sequence
showseqDisplay a sequence with features, translation etc

Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Target users

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

Comments