                                   nthseq



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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

Write to file a single sequence from an input stream of sequences
Version: EMBOSS:6.2.0

   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 and exit. 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
   -version            boolean    Report version number and exit


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
gtgaatgaagtcgcttaagcaatcaatgtcggatgcggcgcgacgcttatccgaccaaca
tatcataacggagtgatcgcattgaacatgccaatgaccgaaagaataagagcaggcaag
ctatttaccgatatgtgcgaaggcttaccggaaaaaagacttcgtgggaaaacgttaatg
tatgagtttaatcactcgcatccatcagaagttgaaaaaagagaaagcctgattaaagaa
atgtttgccacggtaggggaaaacgcctgggtagaaccgcctgtctatttctcttacggt
tccaacatccatataggccgcaatttttatgcaaatttcaatttaaccattgtcgatgac
tacacggtaacaatcggtgataacgtactgattgcacccaacgttactctttccgttacg
ggacaccctgtacaccatgaattgagaaaaaacggcgagatgtactcttttccgataacg
attggcaataacgtctggatcggaagtcatgtggttattaatccaggcgtcaccatcggg
gataattctgttattggcgcgggtagtatcgtcacaaaagacattccaccaaacgtcgtg
gcggctggcgttccttgtcgggttattcgcgaaataaacgaccgggataagcactattat
ttcaaagattataaagttgaatcgtcagtttaaattataaaaattgcctgatacgctgcg
cttatcaggcctacaagttcagcgatctacattagccgcatccggcatgaacaaagcgca
ggaacaagcgtcgcatcatgcctctttgacccacagctgcggaaaacgtactggtgcaaa
acgcagggttatgatcatcagcccaacgacgcacagcgcatgaaatgcccagtccatcag
gtaattgccgctgatactacgcagcacgccagaaaaccacggggcaagcccggcgatgat
aaaaccgattccctgcataaacgccaccagcttgccagcaatagccggttgcacagagtg
atcgagcgccagcagcaaacagagcggaaacgcgccgcccagacctaacccacacaccat
cgcccacaataccggcaattgcatcggcagccagataaagccgcagaaccccaccagttg
taacaccagcgccagcattaacagtttgcgccgatcctgatggcgagccatagcaggcat
cagcaaagctcctgcggcttgcccaagcgtcatcaatgccagtaaggaaccgctgtactg
cgcgctggcaccaatctcaatatagaaagcgggtaaccaggcaatcaggctggcgtaacc
gccgttaatcagaccgaagtaaacacccagcgtccacgcgcggggagtgaataccacgcg
aaccggagtggttgttgtcttgtgggaagaggcgacctcgcgggcgctttgccaccacca
ggcaaagagcgcaacaacggcaggcagcgccaccaggcgagtgtttgataccaggtttcg
ctatgttgaactaaccagggcgttatggcggcaccaagcccaccgccgcccatcagagcc
gcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtttaatcaccgaa
gcatcaccgcctgaatgatgccgatccccaccccaccaagcagtgcgctgctaagcagca
gcgcactttgcgggtaaagctcacgcatcaatgcaccgacggcaatcagcaacagactga
tggcgacactgcgacgttcgctgacatgctgatgaagccagcttccggccagcgccagcc
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
   nthseqset        Reads and writes (returns) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqret           Reads and writes (returns) sequences
   seqretsetall     Reads and writes (returns) many sets of 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
   splitsource      Split sequence(s) into original source sequences
   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 (c) 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
