| skipseq

## Wiki

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Please help by correcting and extending the Wiki pages.

## Function

Read and write (return) sequences, skipping first few

## Description

skipseq is a variant of the standard program for reading and writing sequences, seqret. It performs exactly the same function except that it skips the first specified number of sequences from the input stream and writes out the rest of them. In all other respects, skipseq is the same as seqret. There are many options built-in into EMBOSS for detailed specification of the input and output sequences, for example the sequence type and file format. Optionally, feature information will be read and written.

## Usage

Here is a sample session with skipseq

This does not skip any sequences. It is exactly equivalent to seqret:

    % skipseq
    Read and write (return) sequences, skipping first few
    Input (gapped) sequence(s): @eclac.list
    Number of sequences to skip at start [0]:
    output sequence(s) [j01636.fasta]:

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

Example 2

This skips the first input sequence, writing out the others:

    % skipseq -skip 1
    Read and write (return) sequences, skipping first few
    Input (gapped) sequence(s): @eclac.list
    output sequence(s) [j01636.fasta]:

Go to the output files for this example

## Command line arguments

    Read and write (return) sequences, skipping first few
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                      format, or reference (input USA)
       -skip               integer    [0] Number of sequences to skip at start
                                      (Any integer value)
      [-outseq]            seqoutall  [<sequence>.<format>] Sequence set(s)
                                      filename and optional format (output USA)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -feature            boolean    Use feature information

       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
-skip | integer | Number of sequences to skip at start | Any integer value | 0
[-outseq] (Parameter 2) | seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-feature | boolean | Use feature information | Boolean value Yes/No | No
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 seqoutall 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

skipseq reads one or more nucleotide 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

See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.

## Output file format

skipseq writes one or more sequences files, having optionally skipped the first few sequences.

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.

### Output files for usage example

### File: j01636.fasta

    >J01636 J01636.1 E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
    gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt
    caattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggt
    gtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacg
    cgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaa
    caactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcac
    gcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtg
    gtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatctt
    ctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccatt
    gctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagaca
    cccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctg
    gtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcg
    cgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcg
    gaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaat
    gagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatg
    cgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgac
    gataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaacaggattttcgc
    ctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaag
    ggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacg
    caaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcc
    cgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggc
    accccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggata
    acaatttcacacaggaaacagctatgaccatgattacggattcactggccgtcgttttac
    aacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatcccc
    ctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgc
    gcagcctgaatggcgaatggcgctttgcctggtttccggcaccagaagcggtgccggaaa
    gctggctggagtgcgatcttcctgaggccgatactgtcgtcgtcccctcaaactggcaga
    tgcacggttacgatgcgcccatctacaccaacgtaacctatcccattacggtcaatccgc
    cgtttgttcccacggagaatccgacgggttgttactcgctcacatttaatgttgatgaaa
    gctggctacaggaaggccagacgcgaattatttttgatggcgttaactcggcgtttcatc
    tgtggtgcaacgggcgctgggtcggttacggccaggacagtcgtttgccgtctgaatttg
    acctgagcgcatttttacgcgccggagaaaaccgcctcgcggtgatggtgctgcgttgga
    gtgacggcagttatctggaagatcaggatatgtggcggatgagcggcattttccgtgacg
    tctcgttgctgcataaaccgactacacaaatcagcgatttccatgttgccactcgcttta
    atgatgatttcagccgcgctgtactggaggctgaagttcagatgtgcggcgagttgcgtg
    actacctacgggtaacagtttctttatggcagggtgaaacgcaggtcgccagcggcaccg
    cgcctttcggcggtgaaattatcgatgagcgtggtggttatgccgatcgcgtcacactac
    gtctgaacgtcgaaaacccgaaactgtggagcgccgaaatcccgaatctctatcgtgcgg
    tggttgaactgcacaccgccgacggcacgctgattgaagcagaagcctgcgatgtcggtt
    tccgcgaggtgcggattgaaaatggtctgctgctgctgaacggcaagccgttgctgattc
    gaggcgttaaccgtcacgagcatcatcctctgcatggtcaggtcatggatgagcagacga
    tggtgcaggatatcctgctgatgaagcagaacaactttaacgccgtgcgctgttcgcatt
    atccgaaccatccgctgtggtacacgctgtgcgaccgctacggcctgtatgtggtggatg
    aagccaatattgaaacccacggcatggtgccaatgaatcgtctgaccgatgatccgcgct
    ggctaccggcgatgagcgaacgcgtaacgcgaatggtgcagcgcgatcgtaatcacccga
    gtgtgatcatctggtcgctggggaatgaatcaggccacggcgctaatcacgacgcgctgt
    atcgctggatcaaatctgtcgatccttcccgcccggtgcagtatgaaggcggcggagccg
    acaccacggccaccgatattatttgcccgatgtacgcgcgcgtggatgaagaccagccct
    tcccggctgtgccgaaatggtccatcaaaaaatggctttcgctacctggagagacgcgcc
    cgctgatcctttgcgaatacgcccacgcgatgggtaacagtcttggcggtttcgctaaat

      [Part of this file has been deleted for brevity]

    gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa
    gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt
    gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag
    gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac
    accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg
    ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga
    attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt
    tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga
    gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag
    gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca
    caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg
    gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta
    tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat
    gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg
    tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc
    acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt
    ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat
    cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag
    cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg
    ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg
    gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta
    acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat
    gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct
    tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc
    ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc
    aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac
    gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc
    cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa
    aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag
    ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca
    aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc
    gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt
    aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt
    gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta
    gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg
    cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg
    accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc
    cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg
    cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc
    attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca
    gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac
    gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt
    agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg
    cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta
    gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg
    ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg
    acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc
    cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa
    ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc
    ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg
    tgtcaaaaataataataa

### Output files for usage example 2

### 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
    >V00294 V00294.1 E. coli laci gene (codes for the lac repressor).
    ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca
    gagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtt
    tctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaac
    cgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagt
    ctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactg
    ggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcg
    gtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgac
    caggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtc
    tctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggc
    gtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagt
    tctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaatt
    cagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatg
    caaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcg
    ctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggta
    gtgggatacgacgataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaa
    caggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggc
    caggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctg

      [Part of this file has been deleted for brevity]

    gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa
    gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt
    gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag
    gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac
    accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg
    ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga
    attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt
    tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga
    gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag
    gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca
    caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg
    gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta
    tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat
    gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg
    tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc
    acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt
    ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat
    cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag
    cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg
    ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg
    gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta
    acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat
    gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct
    tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc
    ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc
    aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac
    gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc
    cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa
    aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag
    ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca
    aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc
    gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt
    aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt
    gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta
    gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg
    cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg
    accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc
    cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg
    cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc
    attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca
    gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac
    gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt
    agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg
    cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta
    gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg
    ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg
    acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc
    cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa
    ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc
    ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg
    tgtcaaaaataataataa

See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.

## Data files

None.

## Notes

See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.

seqret has an option to allow it to only read the first sequence from a multiple set of sequences (`-firstonly`). seqret cannot, however, skip the first few sequences from a multiple set of sequence, writing out the rest; this is what skipseq is for.

## References

None.

## Warnings

You may skip all of the input files.
If the -skip value is greater than or equal to the number of input sequences, there is no warning: this is legal.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 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
nthseq | Write to file a single sequence from 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
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

skipseq is a variant of the standard program for reading and writing sequences, seqret.

## Author(s)

Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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

## History

Written (25 June 2002) - Peter Rice

## Target users

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

## Comments

None