EMBOSS: sizeseq

| sizeseq

## Wiki

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Please help by correcting and extending the Wiki pages.

## Function

Sort sequences by size

## Description

sizeseq reads a set of sequences and sorts them by length. By default the sort is in ascending order.

## Usage

Here is a sample session with sizeseq

    % sizeseq -osformat swiss
    Sort sequences by size
    Input sequence set: globins.fasta
    Return longest sequence first [N]:
    output sequence(s) [globins.swiss]:

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

## Command line arguments

    Sort sequences by size
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-sequences]         seqset     Sequence set filename and optional format,
                                      or reference (input USA)
       -descending         boolean    [N] By default the shortest sequence is
                                      given first.
      [-outseq]            seqoutall  [.] Sequence set(s)
                                      filename and optional format (output USA)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -feature            boolean    Sequence feature information will be
                                      retained if this option is set.

       Associated qualifiers:

       "-sequences" 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
[-sequences] (Parameter 1) | seqset | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
-descending | boolean | By default the shortest sequence is given first. | Boolean value Yes/No | No
[-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 | Sequence feature information will be retained if this option is set. | Boolean value Yes/No | No
Associated qualifiers
"-sequences" associated seqset qualifiers
-sbegin1 -sbegin_sequences | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequences | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequences | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequences | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequences | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequences | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequences | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequences | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequences | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequences | string | Input sequence format | Any string |
-iquery1 -iquery_sequences | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequences | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequences | string | Database name | Any string |
-sid1 -sid_sequences | string | Entryname | Any string |
-ufo1 -ufo_sequences | string | UFO features | Any string |
-fformat1 -fformat_sequences | string | Features format | Any string |
-fopenfile1 -fopenfile_sequences | 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

sizeseq 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: globins.fasta

    >HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
    VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
    KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
    EFTPPVQAAYQKVVAGVANALAHKYH
    >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
    VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
    KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
    DFTPELQASYQKVVAGVANALAHKYH
    >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
    VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
    KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
    VHASLDKFLASVSTVLTSKYR
    >HBA_HORSE Sw:Hba_Horse => HBA_HORSE
    VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
    KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
    VHASLDKFLSSVSTVLTSKYR
    >MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
    VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
    LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
    GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
    >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
    PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
    ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
    AVIADTVAAGDAGFEKLMSMICILLRSAY
    >LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
    GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
    QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
    VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

## 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.

sizeseq rewrites the sequences in sorted order.

### Output files for usage example

### File: globins.swiss

    ID   HBA_HUMAN               Reviewed;         141 AA.
    DE   Sw:Hba_Human => HBA_HUMAN
    SQ   SEQUENCE   141 AA;  15126 MW;  34D13618E62A33C1 CRC64;
         VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
         KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
         VHASLDKFLA SVSTVLTSKY R
    //
    ID   HBA_HORSE               Reviewed;         141 AA.
    DE   Sw:Hba_Horse => HBA_HORSE
    SQ   SEQUENCE   141 AA;  15114 MW;  128B9100A4D8457A CRC64;
         VLSAADKTNV KAAWSKVGGH AGEYGAEALE RMFLGFPTTK TYFPHFDLSH GSAQVKAHGK
         KVGDALTLAV GHLDDLPGAL SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA
         VHASLDKFLS SVSTVLTSKY R
    //
    ID   HBB_HUMAN               Reviewed;         146 AA.
    DE   Sw:Hbb_Human => HBB_HUMAN
    SQ   SEQUENCE   146 AA;  15867 MW;  EACBC707CFD466A1 CRC64;
         VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
         KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
         EFTPPVQAAY QKVVAGVANA LAHKYH
    //
    ID   HBB_HORSE               Reviewed;         146 AA.
    DE   Sw:Hbb_Horse => HBB_HORSE
    SQ   SEQUENCE   146 AA;  16008 MW;  734664793DA642EE CRC64;
         VQLSGEEKAA VLALWDKVNE EEVGGEALGR LLVVYPWTQR FFDSFGDLSN PGAVMGNPKV
         KAHGKKVLHS FGEGVHHLDN LKGTFAALSE LHCDKLHVDP ENFRLLGNVL VVVLARHFGK
         DFTPELQASY QKVVAGVANA LAHKYH
    //
    ID   GLB5_PETMA              Reviewed;         149 AA.
    DE   Sw:Glb5_Petma => GLB5_PETMA
    SQ   SEQUENCE   149 AA;  16270 MW;  CD2305FB92DACD59 CRC64;
         PIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE FFPKFKGLTT
         ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD LSGKHAKSFQ VDPQYFKVLA
         AVIADTVAAG DAGFEKLMSM ICILLRSAY
    //
    ID   LGB2_LUPLU              Reviewed;         153 AA.
    DE   Sw:Lgb2_Luplu => LGB2_LUPLU
    SQ   SEQUENCE   153 AA;  16652 MW;  FE29AB9DEF33AFC8 CRC64;
         GALTESQAAL VKSSWEEFNA NIPKHTHRFF ILVLEIAPAA KDLFSFLKGT SEVPQNNPEL
         QAHAGKVFKL VYEAAIQLQV TGVVVTDATL KNLGSVHVSK GVADAHFPVV KEAILKTIKE
         VVGAKWSEEL NSAWTIAYDE LAIVIKKEMN DAA
    //
    ID   MYG_PHYCA               Reviewed;         153 AA.
    DE   Sw:Myg_Phyca => MYG_PHYCA
    SQ   SEQUENCE   153 AA;  17200 MW;  543D385C66FEE1E1 CRC64;
         VLSEGEWQLV LHVWAKVEAD VAGHGQDILI RLFKSHPETL EKFDRFKHLK TEAEMKASED
         LKKHGVTVLT ALGAILKKKG HHEAELKPLA QSHATKHKIP IKYLEFISEA IIHVLHSRHP
         GDFGADAQGA MNKALELFRK DIAAKYKELG YQG
    //

## Data files

None

## Notes

None.

## 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
skipredundant | Remove redundant sequences from an input set
skipseq | Read and write (return) sequences, skipping first few
splitsource | Split sequence(s) into original source sequences
splitter | Split sequence(s) into smaller sequences
trimest | Remove poly-A tails from nucleotide sequences
trimseq | Remove unwanted characters from start and end of sequence(s)
trimspace | Remove extra whitespace from an ASCII text file
union | Concatenate multiple sequences into a single sequence
vectorstrip | Remove vectors from the ends of nucleotide sequence(s)
yank | Add a sequence reference (a full USA) to a list file

## Author(s)

Jon Ison
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

## Target users

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

## Comments

None