EMBOSS: splitter

| splitter

## Wiki

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Please help by correcting and extending the Wiki pages.

## Function

Split sequence(s) into smaller sequences

## Description

splitter splits one or more input sequences into smaller, optionally overlapping, subsequences. The subsequence size and overlap (if any) may be specified. Optionally, feature information will be used.

## Usage

Here is a sample session with splitter

Split a sequence into sub-sequences of 10,000 bases (the default size) with no overlap between the sub-sequences:

    % splitter tembl:BA000025 ba000025.split
    Split sequence(s) into smaller sequences

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

Example 2

Split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence:

    % splitter tembl:BA000025 ba000025.split -size=50000 -over=3000
    Split sequence(s) into smaller sequences

Go to the output files for this example

## Command line arguments

    Split sequence(s) into smaller sequences
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Sequence(s) filename and optional format, or
                                      reference (input USA)
      [-outseq]            seqoutall  [.] Sequence set(s)
                                      filename and optional format (output USA)

       Additional (Optional) qualifiers:
       -size               integer    [10000] Size to split at (Integer 1 or more)
       -overlap            integer    [0] Overlap between split sequences (Integer
                                      0 or more)

       Advanced (Unprompted) qualifiers:
       -feature            boolean    [N] Use feature information
       -addoverlap         boolean    [N] Include overlap in output sequence size

       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
       -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 | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-outseq] (Parameter 2) | seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers
-size | integer | Size to split at | Integer 1 or more | 10000
-overlap | integer | Overlap between split sequences | Integer 0 or more | 0
Advanced (Unprompted) qualifiers
-feature | boolean | Use feature information | Boolean value Yes/No | No
-addoverlap | boolean | Include overlap in output sequence size | 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
-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

splitter 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

'tembl:BA000025' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:BA000025

    ID   BA000025; SV 2; linear; genomic DNA; STD; HUM; 2229817 BP.
    XX
    AC   BA000025; AP000502-AP000521;
    XX
    DT   09-DEC-2004 (Rel. 82, Created)
    DT   17-JUN-2008 (Rel. 96, Last updated, Version 5)
    XX
    DE   Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region.
    XX
    KW   .
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
    OC   Homo.
    XX
    RN   [1]
    RP   1-2229817
    RA   Hirakawa M., Yamaguchi H., Imai K., Shimada J.;
    RT   ;
    RL   Submitted (21-AUG-2001) to the INSDC.
    RL   Mika Hirakawa, Japan Science and Technology Corporation (JST), Advanced
    RL   Databases Department; 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan
    RL   (E-mail:mika@tokyo.jst.go.jp, URL:http://www-alis.tokyo.jst.go.jp/,
    RL   Tel:81-3-5214-8491, Fax:81-3-5214-8470)
    XX
    RN   [2]
    RA   Shiina S., Tamiya G., Oka A., Inoko H.;
    RT   "Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region";
    RL   Unpublished.
    XX
    DR   EPD; EP11158; HS_TNF.
    DR   EPD; EP11159; HS_LTA.
    DR   EPD; EP73522; HS_HLA-B.
    DR   EPD; EP73908; HS_GTF2H4.
    DR   EPD; EP73940; HS_NEU1.
    DR   EPD; EP74013; HS_VARS2.
    DR   EPD; EP74203; HS_MRPS18B.
    DR   EPD; EP74346; HS_HLA-E.
    DR   EPD; EP74389; HS_BAT1.
    DR   EPD; EP74485; HS_IER3.
    DR   Ensembl-Gn; ENSG00000096155; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000096171; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000111971; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000137310; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000137312; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000137313; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000137331; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000137332; Homo_sapiens.
    DR   Ensembl-Gn; ENSG00000137337; Homo_sapiens.

      [Part of this file has been deleted for brevity]

         ttggccccac cccagcatgt ctccaggttc ctctcagccc tggttccttt tggccctgca   2226900
         gtcacaatgg gcaacactgt gacgcaccct gtcctgtgtc acagtgtcat acactcaggc   2226960
         tcacattgcc cctaggccac ttgccagcca agggacatgg ccacattttg tgtcttctgc   2227020
         acctcagcct tgctttcaag tgcaggtgat gatggcaccc acgcagaaca aatgttattt   2227080
         gctatcttcg tcgagtttag tcatccaatt ttccaaccct cactgggcaa ggaagagtgt   2227140
         ggtttccacc aagaaggcag gatgtcagca gtcacagggg caaccaacag ggaaagccgc   2227200
         cggaaaatag accccacagg aagcacaggt gtccagtgga gatgggaacc ctgcagattt   2227260
         gaccgtcttt aagcagatta gagagattac cgttactaac aacttagcca taaaagttta   2227320
         ttagctattt tcaaaaagca taaaattatg taatataatt ttttttaaat ttccatcaat   2227380
         acaaaactaa tctgggcact gcaacttccg gtgggcaact gggataggcg gcatcatcag   2227440
         gaaggcgagc cctgccgtgc cccatgtgcc agtgccccag atggcggcag cctccccaga   2227500
         agcaccttgt atctcccctg cacagggcca gggtcccagc ttcccataca ccttctcctg   2227560
         ctttttcttt tctgtccttt cctttttcaa taaaccacct gcaaaaaggg aaaaccattc   2227620
         tgaggacaag aaacatgtca atgggaaata cacagttgcc agagggtaaa aggccctgtt   2227680
         cattctcatt gaaaagctca ggtatttctg ttaaagtctc tccttttact ttaggatgct   2227740
         gactcctgcg tccatctcaa cctgggcatc gtgccaccac cttcaagaag agaaaaacta   2227800
         agtagtgctt tgcaaagggg cagcagcatt tctcatttct gaccatgtca ggcacatggc   2227860
         catgcagatg agcaggtggg ggacacaggt gagtctccag acctgctctc ctcccacagt   2227920
         acattcttga gtctttttaa acagttgtga aaatgccaca gatgcaagca cctgtgggcc   2227980
         actcccatgg ggaccgttgc acaaggcagt gccactcatt ctcagaacct cctaccatgg   2228040
         gctatgctta gtgacccgag gccaagccaa ggaagacgcc agccacaggg tgccatcctc   2228100
         aggggcatgc tgccagcagg ggcaaagtta tccctagcaa caagatacag aaagaaagaa   2228160
         aaaaggaagg aaatgtagcc aatgggccgg ttcaggttct tgactttgcc acacaaaaga   2228220
         atttgagagc aagtccaaag taaaagtcag caagagaatt tattgcaaag tgaaagtaca   2228280
         ctctgacagc tgatcagagc agctgctcaa aagagagaca gtaccctccc ctcacgggag   2228340
         tcttacatga ttattcatga ataggtggga aggggtattg ttttaagcat gttctgtggt   2228400
         ctcttgaacg tgcatgcact gtggttgtac atatcagcac acacatctta cgtctcatta   2228460
         gcatcttaac ttccctctca gagttgtgtt tgctactatt gtaatgagca taggtcagcc   2228520
         caaggacact attcatgggt ttctgggctt cctcagatgt ggggatgcct cccttggctc   2228580
         ttctacctct ttgctgcagg atgttctaac cacaagccca ggatatggtt tgcgcactgt   2228640
         cgaacagctt gttctctcca tcaacctgac aagtctcttg tttcctttca agggaggctg   2228700
         tgaacaccct atctcactga cctcagaagg acagtacagc agtagccacc atgaccaaaa   2228760
         agatgattcc agaagtgcag gacaactccc tacccagagg ctgtggctgt gcagtaacac   2228820
         accaagaggg gagtccagct ggctctcagg gtgctcacta ccctcatctg ggggcctgga   2228880
         ggacgtcaat tcctgagaac gccacgttct agtgagtaga atgaactgag agatacacag   2228940
         caaagctcca catacttttc cttttctttg tgcccgcagt gttcttcatc agtgtgctct   2229000
         cgcttttcag ctactactgt tggctggctg gaaaaaatag aacaatagta aaaattagag   2229060
         accagtcttt ggtgatgaag agaaatattg gctacttcca gtattttcta gctttggtta   2229120
         tggttgcagt tttccagctc accttgtggg gatgaattca gaaaaaagtt acaaattgaa   2229180
         atgaacatgc cagaagtatt ggctcaaatc aacgttgtcc tattaagcca cttagtgaat   2229240
         caaaagaccg cttgttggac tgttaatctc ggtggccaga gaaaggagct gaagaaggtg   2229300
         ttgccagatc aggaacaaat aattacagcg gcaatagaaa atggaagacc acttgttcat   2229360
         aaccatttga ataagggcaa ggtgtatgga aacacattat gaactgatat tttcagtttt   2229420
         gtttgcaaga aaatgattaa taaggtgaaa taattgaagt atcacggaag atacattaaa   2229480
         aaaaaaaaaa gcctttgtac agtttgctgg agccacagat gtcctactcc agagcagaac   2229540
         aatgcctgaa tcttcagggt ccatttctgc cgcattcact agcaaccaca aatgtgactt   2229600
         aattttactt tggaaataat gcttacccat tgtgagatgc tgtaatatga accatcatta   2229660
         catgttaaca tggcacatgg aattttgagt gtctaagtta catttttaga gttgtttctt   2229720
         agtagccatg tgagtttcca ctccaaaaac acaagctaaa aacttgtttt gagtgaagga   2229780
         catctagggc aaatggtggc tgaaagtgaa tgagatc                            2229817
    //

## 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.

### Output files for usage example

### File: ba000025.split

    >BA000025_1-10000 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region.
    gatctccagagcactcttccctgcagggcaccctcccatcccagactccaggcacctggc
    atgggtggacatctttactttctgggccagcttcagcagagctatgtcatcaccatagaa
    ctccaggattccctggttctttttggcaaagacatcaaaccctggggagatcaccgcctt
    ctcaataaggaattctttgccccactgggatttggggtctcctggaaatgatacactaga
    ttaggctagaccagggctcctgcaggggccagaggctgggtgaggtggtaggatctgtgg
    cttcaggatcaggaggctggtgcatcccctgccttacccacattgaccctccacagggag
    tggtcgttgccatcgcggaagcaatgagctgctgtcaggacccattggtcggagatgagg
    gccccccggcaggtctcttggctcttgggctgcaggggaacaggtgattttcagagattg
    cagtatgtctggcccatggccgcttttacctctggaatccaagccctgcccctccttcct
    ggtaccttaatagtgacatgccagggtgtcctctcctggtcagaggcgtttgctgacatg
    ttccccaccccgcagatggtgtctgtgagcttggagacatctgtgggtgtgaggatcaga
    tggggaaggaggcaagtgaggggcactgtgtccaggttcccaacacgggcctctggcggg
    ctcctcaccatcctccccacaccaaggagggcaaagctcactcacccagcatatgttcaa
    agacctggtgcagagcctttgtgtcctgcagaatgaaggcatgcctctcaccatccttct
    tggaccctagctcattcagttctctccagtccacatccagcttgcccaccccgatggcat
    agatgtctggtggggaagagggaaatcaccagactcctgtggctttggggctaccccatg
    agacaggaggctgtcatctgaaactcactgtgtccaatcaagacctacatgagctggacc
    cctgcgtcctccccactgctacctgtctgccttcatttcctgccactccctgcccttcac
    tctcctgcagcacacagcctctttgaagttcctcaaatccataggcatggtcacacctca
    ggccctttgcccagctgtgcctctgcctagttcactcctcccccccagacttccacatgg
    ctcactttcgtacctttttaagtcttggctcaaatgtcaccttctcagtgaggccttccc
    tggtcttcctgtctaaaactgcaatgccccagacaaactttcatccccactttgggaggc
    aaggtgggaggatcccttgaagccagaagtttgagaccagcctgggcaacatggcaacac
    cccttagcttgtgtcacctaccacctgctgggttctatggttttcttatcctgtttattc
    cctgtaatggtggaattgtgtcccccagaaagatgtgttcgagtcctaatccccagtatc
    tgtgactttatttggaaaaagggtctttgcagatgtaatcaagttaagattaagtcatac
    tagattagggtgagctctaatccaatgactgaggtccttataagaagaggtaagccagag
    ccaggcgtggtggctcacacctgtaatcaccaggaggcggtggttgtggtgagccaagat
    cgcgccattgcactccagcctgggcaacaagagcaaaaccccgtctcaaaaaaaaaaaaa
    gaagaggtgagccgggcacggtggctcacacctgtaatcccagcactctgggaggctgag
    gcgggcagatcacgaggtcaggaattcaagaccagcctgaccaacatggtgaaaccctgt
    ctctactaaaaatacaaaaattagccagacatgctggcacacacctgtaatcccagctac
    tcaggaggctgaggcaggagaatcgcttgaaccgggaggcggatgttgcagtgagccgag
    attgcaccactgcactccagcctgggcaacagagcaagactccatctcaaaaaaaaaaaa
    aaaaaaaaaaagtgaactggctgggcatggtggtgactcatgcctgtaatcccggcagtt
    tttttgaggcgaaggcaggcagatcgccttgaggccaggagtttaagaccagcctagcca
    acatggcgagaccatgtctctactaaaaatacaaaaatttgccgggcatggtggcacatg
    cctgtaatcccagcttcttgggagactgaggcacgagaatcacctgaacccaggaggcag
    aggttacagtgagccgggatcccgccactgcactgcagcctgggcttctgggtgacagag
    cgagactctgtctcaaacaaatgaacagaaaaagaagaaaggaatttggacacaaagaca
    caggtagtgggtctcctatctatataagagaacagcatgtaatgacacagaggcacacac
    agaaaagaaggcgagttgaagacagaggcagagaatgggtttatgctgccgcaagccaag
    gttggagctgccggcagccggaaaaggcaggaaagaattcttcccaagagccttctgagg
    aagcacggccctgccaacaccttgatttcagacttctaacctccagaactgtaagaaaaa
    gaaattctgtgttctaagccacccaggtttgtggtagtttggtaagtacttttaaatgac
    tgaatgaatagaaagaactcagaacacaacatggaaactaaacctcagatctggtcttcc
    tctgtaaaaggtagcatctgggagaagggcctaaagccacgttttcccactggaggccct
    ggacccacacaacaggccgcgcctgtcctccgactgtggtgccagtcagaactgccctca
    gacagaccacagagtctactcctctcccagcctttgcaccccttgtggcccatttttgtt

      [Part of this file has been deleted for brevity]

    cctcggtctgtctccaccaggccctgtgagggtgggtggaggctctctccaagccctcgt
    ttggccccaccccagcatgtctccaggttcctctcagccctggttccttttggccctgca
    gtcacaatgggcaacactgtgacgcaccctgtcctgtgtcacagtgtcatacactcaggc
    tcacattgcccctaggccacttgccagccaagggacatggccacattttgtgtcttctgc
    acctcagccttgctttcaagtgcaggtgatgatggcacccacgcagaacaaatgttattt
    gctatcttcgtcgagtttagtcatccaattttccaaccctcactgggcaaggaagagtgt
    ggtttccaccaagaaggcaggatgtcagcagtcacaggggcaaccaacagggaaagccgc
    cggaaaatagaccccacaggaagcacaggtgtccagtggagatgggaaccctgcagattt
    gaccgtctttaagcagattagagagattaccgttactaacaacttagccataaaagttta
    ttagctattttcaaaaagcataaaattatgtaatataattttttttaaatttccatcaat
    acaaaactaatctgggcactgcaacttccggtgggcaactgggataggcggcatcatcag
    gaaggcgagccctgccgtgccccatgtgccagtgccccagatggcggcagcctccccaga
    agcaccttgtatctcccctgcacagggccagggtcccagcttcccatacaccttctcctg
    ctttttcttttctgtcctttcctttttcaataaaccacctgcaaaaagggaaaaccattc
    tgaggacaagaaacatgtcaatgggaaatacacagttgccagagggtaaaaggccctgtt
    cattctcattgaaaagctcaggtatttctgttaaagtctctccttttactttaggatgct
    gactcctgcgtccatctcaacctgggcatcgtgccaccaccttcaagaagagaaaaacta
    agtagtgctttgcaaaggggcagcagcatttctcatttctgaccatgtcaggcacatggc
    catgcagatgagcaggtgggggacacaggtgagtctccagacctgctctcctcccacagt
    acattcttgagtctttttaaacagttgtgaaaatgccacagatgcaagcacctgtgggcc
    actcccatggggaccgttgcacaaggcagtgccactcattctcagaacctcctaccatgg
    gctatgcttagtgacccgaggccaagccaaggaagacgccagccacagggtgccatcctc
    aggggcatgctgccagcaggggcaaagttatccctagcaacaagatacagaaagaaagaa
    aaaaggaaggaaatgtagccaatgggccggttcaggttcttgactttgccacacaaaaga
    atttgagagcaagtccaaagtaaaagtcagcaagagaatttattgcaaagtgaaagtaca
    ctctgacagctgatcagagcagctgctcaaaagagagacagtaccctcccctcacgggag
    tcttacatgattattcatgaataggtgggaaggggtattgttttaagcatgttctgtggt
    ctcttgaacgtgcatgcactgtggttgtacatatcagcacacacatcttacgtctcatta
    gcatcttaacttccctctcagagttgtgtttgctactattgtaatgagcataggtcagcc
    caaggacactattcatgggtttctgggcttcctcagatgtggggatgcctcccttggctc
    ttctacctctttgctgcaggatgttctaaccacaagcccaggatatggtttgcgcactgt
    cgaacagcttgttctctccatcaacctgacaagtctcttgtttcctttcaagggaggctg
    tgaacaccctatctcactgacctcagaaggacagtacagcagtagccaccatgaccaaaa
    agatgattccagaagtgcaggacaactccctacccagaggctgtggctgtgcagtaacac
    accaagaggggagtccagctggctctcagggtgctcactaccctcatctgggggcctgga
    ggacgtcaattcctgagaacgccacgttctagtgagtagaatgaactgagagatacacag
    caaagctccacatacttttccttttctttgtgcccgcagtgttcttcatcagtgtgctct
    cgcttttcagctactactgttggctggctggaaaaaatagaacaatagtaaaaattagag
    accagtctttggtgatgaagagaaatattggctacttccagtattttctagctttggtta
    tggttgcagttttccagctcaccttgtggggatgaattcagaaaaaagttacaaattgaa
    atgaacatgccagaagtattggctcaaatcaacgttgtcctattaagccacttagtgaat
    caaaagaccgcttgttggactgttaatctcggtggccagagaaaggagctgaagaaggtg
    ttgccagatcaggaacaaataattacagcggcaatagaaaatggaagaccacttgttcat
    aaccatttgaataagggcaaggtgtatggaaacacattatgaactgatattttcagtttt
    gtttgcaagaaaatgattaataaggtgaaataattgaagtatcacggaagatacattaaa
    aaaaaaaaaagcctttgtacagtttgctggagccacagatgtcctactccagagcagaac
    aatgcctgaatcttcagggtccatttctgccgcattcactagcaaccacaaatgtgactt
    aattttactttggaaataatgcttacccattgtgagatgctgtaatatgaaccatcatta
    catgttaacatggcacatggaattttgagtgtctaagttacatttttagagttgtttctt
    agtagccatgtgagtttccactccaaaaacacaagctaaaaacttgttttgagtgaagga
    catctagggcaaatggtggctgaaagtgaatgagatc

### Output files for usage example 2

### File: ba000025.split

    >BA000025_1-50000 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region.
    gatctccagagcactcttccctgcagggcaccctcccatcccagactccaggcacctggc
    atgggtggacatctttactttctgggccagcttcagcagagctatgtcatcaccatagaa
    ctccaggattccctggttctttttggcaaagacatcaaaccctggggagatcaccgcctt
    ctcaataaggaattctttgccccactgggatttggggtctcctggaaatgatacactaga
    ttaggctagaccagggctcctgcaggggccagaggctgggtgaggtggtaggatctgtgg
    cttcaggatcaggaggctggtgcatcccctgccttacccacattgaccctccacagggag
    tggtcgttgccatcgcggaagcaatgagctgctgtcaggacccattggtcggagatgagg
    gccccccggcaggtctcttggctcttgggctgcaggggaacaggtgattttcagagattg
    cagtatgtctggcccatggccgcttttacctctggaatccaagccctgcccctccttcct
    ggtaccttaatagtgacatgccagggtgtcctctcctggtcagaggcgtttgctgacatg
    ttccccaccccgcagatggtgtctgtgagcttggagacatctgtgggtgtgaggatcaga
    tggggaaggaggcaagtgaggggcactgtgtccaggttcccaacacgggcctctggcggg
    ctcctcaccatcctccccacaccaaggagggcaaagctcactcacccagcatatgttcaa
    agacctggtgcagagcctttgtgtcctgcagaatgaaggcatgcctctcaccatccttct
    tggaccctagctcattcagttctctccagtccacatccagcttgcccaccccgatggcat
    agatgtctggtggggaagagggaaatcaccagactcctgtggctttggggctaccccatg
    agacaggaggctgtcatctgaaactcactgtgtccaatcaagacctacatgagctggacc
    cctgcgtcctccccactgctacctgtctgccttcatttcctgccactccctgcccttcac
    tctcctgcagcacacagcctctttgaagttcctcaaatccataggcatggtcacacctca
    ggccctttgcccagctgtgcctctgcctagttcactcctcccccccagacttccacatgg
    ctcactttcgtacctttttaagtcttggctcaaatgtcaccttctcagtgaggccttccc
    tggtcttcctgtctaaaactgcaatgccccagacaaactttcatccccactttgggaggc
    aaggtgggaggatcccttgaagccagaagtttgagaccagcctgggcaacatggcaacac
    cccttagcttgtgtcacctaccacctgctgggttctatggttttcttatcctgtttattc
    cctgtaatggtggaattgtgtcccccagaaagatgtgttcgagtcctaatccccagtatc
    tgtgactttatttggaaaaagggtctttgcagatgtaatcaagttaagattaagtcatac
    tagattagggtgagctctaatccaatgactgaggtccttataagaagaggtaagccagag
    ccaggcgtggtggctcacacctgtaatcaccaggaggcggtggttgtggtgagccaagat
    cgcgccattgcactccagcctgggcaacaagagcaaaaccccgtctcaaaaaaaaaaaaa
    gaagaggtgagccgggcacggtggctcacacctgtaatcccagcactctgggaggctgag
    gcgggcagatcacgaggtcaggaattcaagaccagcctgaccaacatggtgaaaccctgt
    ctctactaaaaatacaaaaattagccagacatgctggcacacacctgtaatcccagctac
    tcaggaggctgaggcaggagaatcgcttgaaccgggaggcggatgttgcagtgagccgag
    attgcaccactgcactccagcctgggcaacagagcaagactccatctcaaaaaaaaaaaa
    aaaaaaaaaaagtgaactggctgggcatggtggtgactcatgcctgtaatcccggcagtt
    tttttgaggcgaaggcaggcagatcgccttgaggccaggagtttaagaccagcctagcca
    acatggcgagaccatgtctctactaaaaatacaaaaatttgccgggcatggtggcacatg
    cctgtaatcccagcttcttgggagactgaggcacgagaatcacctgaacccaggaggcag
    aggttacagtgagccgggatcccgccactgcactgcagcctgggcttctgggtgacagag
    cgagactctgtctcaaacaaatgaacagaaaaagaagaaaggaatttggacacaaagaca
    caggtagtgggtctcctatctatataagagaacagcatgtaatgacacagaggcacacac
    agaaaagaaggcgagttgaagacagaggcagagaatgggtttatgctgccgcaagccaag
    gttggagctgccggcagccggaaaaggcaggaaagaattcttcccaagagccttctgagg
    aagcacggccctgccaacaccttgatttcagacttctaacctccagaactgtaagaaaaa
    gaaattctgtgttctaagccacccaggtttgtggtagtttggtaagtacttttaaatgac
    tgaatgaatagaaagaactcagaacacaacatggaaactaaacctcagatctggtcttcc
    tctgtaaaaggtagcatctgggagaagggcctaaagccacgttttcccactggaggccct
    ggacccacacaacaggccgcgcctgtcctccgactgtggtgccagtcagaactgccctca
    gacagaccacagagtctactcctctcccagcctttgcaccccttgtggcccatttttgtt

      [Part of this file has been deleted for brevity]

    ggagaggggcaggtgcccctcctcggtctgtctccaccaggccctgtgagggtgggtgga
    ggctctctccaagccctcgtttggccccaccccagcatgtctccaggttcctctcagccc
    tggttccttttggccctgcagtcacaatgggcaacactgtgacgcaccctgtcctgtgtc
    acagtgtcatacactcaggctcacattgcccctaggccacttgccagccaagggacatgg
    ccacattttgtgtcttctgcacctcagccttgctttcaagtgcaggtgatgatggcaccc
    acgcagaacaaatgttatttgctatcttcgtcgagtttagtcatccaattttccaaccct
    cactgggcaaggaagagtgtggtttccaccaagaaggcaggatgtcagcagtcacagggg
    caaccaacagggaaagccgccggaaaatagaccccacaggaagcacaggtgtccagtgga
    gatgggaaccctgcagatttgaccgtctttaagcagattagagagattaccgttactaac
    aacttagccataaaagtttattagctattttcaaaaagcataaaattatgtaatataatt
    ttttttaaatttccatcaatacaaaactaatctgggcactgcaacttccggtgggcaact
    gggataggcggcatcatcaggaaggcgagccctgccgtgccccatgtgccagtgccccag
    atggcggcagcctccccagaagcaccttgtatctcccctgcacagggccagggtcccagc
    ttcccatacaccttctcctgctttttcttttctgtcctttcctttttcaataaaccacct
    gcaaaaagggaaaaccattctgaggacaagaaacatgtcaatgggaaatacacagttgcc
    agagggtaaaaggccctgttcattctcattgaaaagctcaggtatttctgttaaagtctc
    tccttttactttaggatgctgactcctgcgtccatctcaacctgggcatcgtgccaccac
    cttcaagaagagaaaaactaagtagtgctttgcaaaggggcagcagcatttctcatttct
    gaccatgtcaggcacatggccatgcagatgagcaggtgggggacacaggtgagtctccag
    acctgctctcctcccacagtacattcttgagtctttttaaacagttgtgaaaatgccaca
    gatgcaagcacctgtgggccactcccatggggaccgttgcacaaggcagtgccactcatt
    ctcagaacctcctaccatgggctatgcttagtgacccgaggccaagccaaggaagacgcc
    agccacagggtgccatcctcaggggcatgctgccagcaggggcaaagttatccctagcaa
    caagatacagaaagaaagaaaaaaggaaggaaatgtagccaatgggccggttcaggttct
    tgactttgccacacaaaagaatttgagagcaagtccaaagtaaaagtcagcaagagaatt
    tattgcaaagtgaaagtacactctgacagctgatcagagcagctgctcaaaagagagaca
    gtaccctcccctcacgggagtcttacatgattattcatgaataggtgggaaggggtattg
    ttttaagcatgttctgtggtctcttgaacgtgcatgcactgtggttgtacatatcagcac
    acacatcttacgtctcattagcatcttaacttccctctcagagttgtgtttgctactatt
    gtaatgagcataggtcagcccaaggacactattcatgggtttctgggcttcctcagatgt
    ggggatgcctcccttggctcttctacctctttgctgcaggatgttctaaccacaagccca
    ggatatggtttgcgcactgtcgaacagcttgttctctccatcaacctgacaagtctcttg
    tttcctttcaagggaggctgtgaacaccctatctcactgacctcagaaggacagtacagc
    agtagccaccatgaccaaaaagatgattccagaagtgcaggacaactccctacccagagg
    ctgtggctgtgcagtaacacaccaagaggggagtccagctggctctcagggtgctcacta
    ccctcatctgggggcctggaggacgtcaattcctgagaacgccacgttctagtgagtaga
    atgaactgagagatacacagcaaagctccacatacttttccttttctttgtgcccgcagt
    gttcttcatcagtgtgctctcgcttttcagctactactgttggctggctggaaaaaatag
    aacaatagtaaaaattagagaccagtctttggtgatgaagagaaatattggctacttcca
    gtattttctagctttggttatggttgcagttttccagctcaccttgtggggatgaattca
    gaaaaaagttacaaattgaaatgaacatgccagaagtattggctcaaatcaacgttgtcc
    tattaagccacttagtgaatcaaaagaccgcttgttggactgttaatctcggtggccaga
    gaaaggagctgaagaaggtgttgccagatcaggaacaaataattacagcggcaatagaaa
    atggaagaccacttgttcataaccatttgaataagggcaaggtgtatggaaacacattat
    gaactgatattttcagttttgtttgcaagaaaatgattaataaggtgaaataattgaagt
    atcacggaagatacattaaaaaaaaaaaaagcctttgtacagtttgctggagccacagat
    gtcctactccagagcagaacaatgcctgaatcttcagggtccatttctgccgcattcact
    agcaaccacaaatgtgacttaattttactttggaaataatgcttacccattgtgagatgc
    tgtaatatgaaccatcattacatgttaacatggcacatggaattttgagtgtctaagtta
    catttttagagttgtttcttagtagccatgtgagtttccactccaaaaacacaagctaaa
    aacttgttttgagtgaaggacatctagggcaaatggtggctgaaagtgaatgagatc

The names of the sequences are the same as the original sequence, with '_start-end' appended, where 'start', and 'end' are the start and end positions of the sub-sequence. eg: The name U01317 would be changed in the sub-sequences to: U01317_1-50000 and U01317_50001-73308 if they were split at the size of 50000 with no overlap.

## Data files

None.

## Notes

Splitting a large sequence into smaller sub-sequences for analysis might be useful in cases where a particularly memory or CPU intensive application will not run quickly enough or at all on the full sequence. This should seldom be necessary in EMBOSS.

By default, splitter will write all the sub-sequences to a single file. In some cases, particularly where non-EMBOSS programs are used, it is necessary to have a single sequence per file. To write the sub-sequences into separate files use the command-line switch `-ossingle`.

## References

None

## Warnings

None.

## 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
skipseq | Read and write (return) sequences, skipping first few
splitsource | Split sequence(s) into original source 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

## 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

Completed 22 March 1999

## Target users

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

## Comments

None