
                                  nthseq 



Function

   Write to file a single sequence from an input stream of sequences

Description

   nthseq writes to file a single sequence from an input stream of
   sequences. The sequence is specified by number, which is the order it
   appears in the input file. The output file name may be specified.

Usage

   Here is a sample session with nthseq


% nthseq 
Write to file a single sequence from an input stream of sequences
Input (gapped) sequence(s): @eclac.list
The number of the sequence to output [1]: 2
output sequence [j01636.fasta]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
   -number             integer    [1] The number of the sequence to output
                                  (Integer 1 or more)
  [-outseq]            seqout     [.] Sequence filename and
                                  optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 dying program messages

Input file format

   nthseq reads a a normal sequence USA.

  Input files for usage example

  File: eclac.list

#Formerly ECLAC
tembl:J01636

#Formerly ECLACA
tembl:X51872

#Formerly ECLACI
tembl:V00294

#Formerly ECLACY
tembl:V00295

#Formerly ECLACZ
tembl:V00296

Output file format

   The output is the specified ordinal sequence from the input USA.

   In the example, the second sequence from the input file will be
   written out to the specified output file.

  Output files for usage example

  File: j01636.fasta

>X51872 X51872.1 Escherichia coli lacA gene for thiogalactoside transacetylase

cgcccatggtaaccaccggcagagcggtcgac

Data files

   None.

Notes

   In EMBOSS, when an application has to write out many sequences, they
   are typically all written to a single file. This default behaviour can
   be changed by using the qualifier -ossingle which forces each sequence
   to be written to its own file.

   The program seqretsplit will take a file containing many sequences and
   will output many files, each containing one sequence. However you have
   no choice over the naming of the files - they are named after the ID
   name fo the sequence they contain.

   It may be useful to use this application in a small script that
   extracts all sequences from a multiple sequence file and explicitly
   names the output files in the way that you require.

   For example:

#!/usr/local/bin/perl -w
if ($#ARGV !=1) {
  die "Usage: scriptname in out\n";
}
$count=1;
@list = `infoseq $ARGV[0] -auto -only -name`;
while ($count <= $#list+1) {
  system("nthseq -auto $ARGV[0] -n $count $ARGV[1]-$count.seq");
  $count++;
}

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name Description
   aligncopy Reads and writes alignments
   aligncopypair Reads and writes pairs from alignments
   biosed Replace or delete sequence sections
   codcopy Copy and reformat a codon usage table
   cutseq Removes a section from a sequence
   degapseq Removes non-alphabetic (e.g. gap) characters from sequences
   descseq Alter the name or description of a sequence
   entret Retrieves sequence entries from flatfile databases and files
   extractalign Extract regions from a sequence alignment
   extractfeat Extract features from sequence(s)
   extractseq Extract regions from a sequence
   featcopy Reads and writes a feature table
   featreport Reads and writes a feature table
   listor Write a list file of the logical OR of two sets of sequences
   makenucseq Create random nucleotide sequences
   makeprotseq Create random protein sequences
   maskambignuc Masks all ambiguity characters in nucleotide sequences
   with N
   maskambigprot Masks all ambiguity characters in protein sequences with
   X
   maskfeat Write a sequence with masked features
   maskseq Write a sequence with masked regions
   newseq Create a sequence file from a typed-in sequence
   nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn Remove carriage return from ASCII files
   nospace Remove all whitespace from an ASCII text file
   notab Replace tabs with spaces in an ASCII text file
   notseq Write to file a subset of an input stream of sequences
   pasteseq Insert one sequence into another
   revseq Reverse and complement a nucleotide sequence
   seqret Reads and writes (returns) sequences
   seqretsplit Reads sequences and writes them to individual files
   sizeseq Sort sequences by size
   skipredundant Remove redundant sequences from an input set
   skipseq Reads and writes (returns) sequences, skipping first few
   splitter Split sequence(s) into smaller sequences
   trimest Remove poly-A tails from nucleotide sequences
   trimseq Remove unwanted characters from start and end of sequence(s)
   trimspace Remove extra whitespace from an ASCII text file
   union Concatenate multiple sequences into a single sequence
   vectorstrip Removes vectors from the ends of nucleotide sequence(s)
   yank Add a sequence reference (a full USA) to a list file

   The program seqretsplit will take a file containing many sequences and
   will output many files, each containing one sequence. However you have
   no choice over the naming of the files - they are named after the ID
   name fo the sequence they contain.

Author(s)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Written (2000) - Gary Williams

Target users

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

Comments

   None
