
                                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 tembl:hsfa* 
Reads and writes (returns) sequences in individual files
Output sequence [hsfau.fasta]: 
   
   Go to the input files for this example
   Go to the output files for this example
   
   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

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

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -firstonly          boolean    Read one sequence and stop

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    First base used
   -send1               integer    Last base used, def=seq length
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outseq" associated qualifiers
   -osformat2           string     Output seq format
   -osextension2        string     File name extension
   -osname2             string     Base file name
   -osdirectory2        string     Output directory
   -osdbname2           string     Database name to add
   -ossingle2           boolean    Separate file for each entry
   -oufo2               string     UFO features
   -offormat2           string     Features format
   -ofname2             string     Features file name
   -ofdirectory2        string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths
   

   Standard (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
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -firstonly Read one sequence and stop Boolean value Yes/No No
   
Input file format

   seqretsplit reads a normal sequence USA.
   
  Input files for usage example
  
   'tembl:hsfa*' is a sequence entry in the example nucleic acid database
   'tembl'
   
Output file format

  Output files for usage example
  
  File: hsfau.fasta
  
>HSFAU X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa
   
  File: hsfau1.fasta
  
>HSFAU1 X65921.1 H.sapiens fau 1 gene
ctaccattttccctctcgattctatatgtacactcgggacaagttctcctgatcgaaaac
ggcaaaactaaggccccaagtaggaatgccttagttttcggggttaacaatgattaacac
tgagcctcacacccacgcgatgccctcagctcctcgctcagcgctctcaccaacagccgt
agcccgcagccccgctggacaccggttctccatccccgcagcgtagcccggaacatggta
gctgccatctttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgccccg
tcctgcgcgagctgctgcccaggcaggttcgccggtgcgagcgtaaaggggcggagctag
gactgccttgggcggtacaaatagcagggaaccgcgcggtcgctcagcagtgacgtgaca
cgcagcccacggtctgtactgacgcgccctcgcttcttcctctttctcgactccatcttc
gcggtagctgggaccgccgttcaggtaagaatggggccttggctggatccgaagggcttg
tagcaggttggctgcggggtcagaaggcgcggggggaaccgaagaacggggcctgctccg
tggccctgctccagtccctatccgaactccttgggaggcactggccttccgcacgtgagc
cgccgcgaccaccatcccgtcgcgatcgtttctggaccgctttccactcccaaatctcct
ttatcccagagcatttcttggcttctcttacaagccgtcttttctttactcagtcgccaa
tatgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaac
ggtcgcccagatcaaggtaaggctgcttggtgcgccctgggttccattttcttgtgctct
tcactctcgcggcccgagggaacgcttacgagccttatctttccctgtaggctcatgtag
cctcactggagggcattgccccggaagatcaagtcgtgctcctggcaggcgcgcccctgg
aggatgaggccactctgggccagtgcggggtggaggccctgactaccctggaagtagcag
gccgcatgcttggaggtgagtgagagaggaatgttctttgaagtaccggtaagcgtctag
tgagtgtggggtgcatagtcctgacagctgagtgtcacacctatggtaatagagtacttc
tcactgtcttcagttcagagtgattcttcctgtttacatccctcatgttgaacacagacg
tccatgggagactgagccagagtgtagttgtatttcagtcacatcacgagatcctagtct
ggttatcagcttccacactaaaaattaggtcagaccaggccccaaagtgctctataaatt
agaagctggaagatcctgaaatgaaacttaagatttcaaggtcaaatatctgcaactttg
ttctcattacctattgggcgcagcttctctttaaaggcttgaattgagaaaagaggggtt
ctgctgggtggcaccttcttgctcttacctgctggtgccttcctttcccactacaggtaa
agtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaaggtgagtga
gagtattagtggtcatggtgttaggactttttttcctttcacagctaaaccaagtccctg
ggctcttactcggtttgccttctccctccctggagatgagcctgagggaagggatgctag
gtgtggaagacaggaaccagggcctgattaaccttcccttctccaggtggccaaacagga
gaagaagaagaagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgt
caacgttgtgcccacctttggcaagaagaagggccccaatgccaactcttaagtcttttg
taattctggctttctctaataaaaaagccacttagttcagtcatcgcattgtttcatctt
tacttgcaaggcctcagggagaggtgtgcttctcgg
   
   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
   skipseq      Reads and writes (returns) sequences, skipping the first few
   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)

   Peter Rice (pmr  ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, 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
