
                            EMBOSS: seqretsplit
     _________________________________________________________________
   
                              Program seqretsplit
                                       
Function

   Reads and writes (returns) sequences in individual files
   
Description

   seqretsplit is exactly the same as the program seqret except that when
   it writes out more than one sequence, it writes each sequence to an
   individual file.
   
   Its main use is therefore to split a file containing multiple
   sequences into many files, each containing one sequence.
   
   The names of the files it creates are derived from the ID name of the
   sequence, followed by an extension denoting the format of the
   sequence. You have no control over the names of the files it writes
   out.
   
   For example, if the files embl:hsfa11* are read in and the output is
   specified as wibble.seq, then the following files are expected to be
   created:
   
hsfa110.fasta
hsfa111.fasta
hsfa112.fasta
hsfa113.fasta
hsfa114.fasta

   (No file wibble.seq is created.)
   
   Why would you want to split a multiple sequence file into many
   individual files?
   
   EMBOSS programs can read in many sequences from one file where this is
   sensible. Sometimes EMBOSS programs can only read in one sequence at a
   time because that is the sensible way to do things, but your sequence
   is one sequence of many in a file. You can specify that sequence using
   the USA filename:sequenceID, but you may still feel more comfortable
   splitting your sequences up into many files first.
   
   Many non-EMBOSS programs will also have restrictions on whether they
   can read in multiple sequence files or not.
   
Usage

   Here is a sample session with seqretsplit:

% seqretsplit
Reads and writes (returns) sequences in individual files
Input sequence(s): embl:hsfa11*
Output sequence [hsfa110.fasta]:

   The specification of the output file is not used in this case.
   
   At some point this ought to change and you will not be prompted for
   the output file at all.
   
Command line arguments

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

   Optional qualifiers: (none)
   Advanced qualifiers:
   -firstonly          bool       Read one sequence and stop

   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
   -firstonly Read one sequence and stop Yes/No No
   
Input file format

   Normal sequence USA.
   
Output file format

   One file for each input sequence is written out.
   
   The names of the files it creates are derived from the ID name of the
   sequence, followed by an extension denoting the format of the
   sequence. You have no control over the names of the files it writes
   out.
   
   For example, if the files embl:hsfa11* are read in and the output is
   specified as wibble.seq, then the following files are expected to be
   created:
   
hsfa110.fasta
hsfa111.fasta
hsfa112.fasta
hsfa113.fasta
hsfa114.fasta

   (No file wibble.seq is created.)
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   It shouldn't really prompt for the output filename.
   
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
   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
   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
   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 Peter Rice (price@hgmp.mrc.ac.uk)
   
History

   Written (Jan 2000) - Peter Rice
   
Target users

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