| nthseq

## Wiki

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Please help by correcting and extending the Wiki pages.

## 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:6.6.0.0

       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
       -scircular1         boolean    Sequence is circular
       -squick1            boolean    Read id and sequence only
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqall | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
-number | integer | The number of the sequence to output | Integer 1 or more | 1
[-outseq] (Parameter 2) | seqout | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outseq" associated seqout qualifiers
-osformat2 -osformat_outseq | string | Output seq format | Any string |
-osextension2 -osextension_outseq | string | File name extension | Any string |
-osname2 -osname_outseq | string | Base file name | Any string |
-osdirectory2 -osdirectory_outseq | string | Output directory | Any string |
-osdbname2 -osdbname_outseq | string | Database name to add | Any string |
-ossingle2 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo2 -oufo_outseq | string | UFO features | Any string |
-offormat2 -offormat_outseq | string | Features format | Any string |
-ofname2 -ofname_outseq | string | Features file name | Any string |
-ofdirectory2 -ofdirectory_outseq | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

nthseq reads one or more nucleotiode or protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### 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 a standard EMBOSS sequence file.

The results can be output in one of several styles by using the command-line qualifier `-osformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

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 | Read and write alignments
aligncopypair | Read and write pairs from alignments
biosed | Replace or delete sequence sections
codcopy | Copy and reformat a codon usage table
cutseq | Remove a section from a sequence
degapseq | Remove non-alphabetic (e.g. gap) characters from sequences
descseq | Alter the name or description of a sequence
entret | Retrieve 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 | Read and write a feature table
featmerge | Merge two overlapping feature tables
featreport | Read and write a feature table
feattext | Return a feature table original text
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 | Mask all ambiguity characters in nucleotide sequences with N
maskambigprot | Mask 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 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 | Read and write (return) one set of sequences from many
pasteseq | Insert one sequence into another
revseq | Reverse and complement a nucleotide sequence
seqcount | Read and count sequences
seqret | Read and write (return) sequences
seqretsetall | Read and write (return) many sets of sequences
seqretsplit | Read sequences and write them to individual files
sizeseq | Sort sequences by size
skipredundant | Remove redundant sequences from an input set
skipseq | Read and write (return) 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 | Remove 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 formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## 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