
                             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)
   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
   [-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 name                          Description
   biosed       Replace or delete sequence sections
   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
   infoseq      Displays some simple information about sequences
   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
   seqretset    Reads and writes (returns) a set of sequences all at once
   seqretsplit  Reads and writes (returns) sequences in individual files
   splitter     Split a sequence into (overlapping) smaller sequences
   swissparse   Retrieves sequences from swissprot using keyword search
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   vectorstrip  Strips out DNA between a pair of vector sequences
   
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
