splitter

 

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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:6.4.0.0

   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
   -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

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
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-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 EMBL/GenBank/DDBJ databases.
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   GDB; 11515913.
DR   GOA; P59942.
DR   HGNC; 20668; MCCD1.
DR   IMGT/HLA; HLA02629; J*01:01:01:02.
DR   IMGT/HLA; HLA02802; V*01:01:01:02.
DR   RFAM; RF00017; SRP_euk_arch.
DR   RFAM; RF00019; Y_RNA.
DR   RFAM; RF00026; U6.
DR   RFAM; RF00100; 7SK.


  [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 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
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 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 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 Reads and writes (returns) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Reads and counts sequences
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
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

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