EMBOSS: seqretall


Program seqretall

Function

Reads and writes (returns) a set of sequences one at a time

Description

This application is now replaced by "seqret" which is the same.

In early pre-release versions of EMBOSS, seqret read only one sequence so this program was needed to read more sequences. We have retained it for compatibility only.

Usage

Here is a sample session with seqretall.

% seqretall
Reads and writes (returns) a set of sequences one at a time
Input sequence(s): embl:eclac*
Output sequence [eclac.fasta]: 

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outseq]            seqoutall  Output sequence(s) USA

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

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

Input file format

Output file format

The output from seqretall 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, for example if you try to read the output from the example run with seqretall and give no output format.

As seqretall reads only the first sequence before opening the output file it will overwrite the sequences before reading has completed, with unpredictable result. Note that this is not true of seqretset which reads all sequences into memory 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
seqretsetReads and writes (returns) a set of sequences all at once
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