                                   sizeseq



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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:6.2.0

   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
   -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


Input file format

   sizeseq reads any normal sequence USAs.

  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

   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        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
   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 all 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
   seqret           Reads and writes (returns) sequences
   seqretsetall     Reads and writes (returns) many sets of sequences
   seqretsplit      Reads sequences and writes them to individual files
   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
   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      Removes vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

Author(s)

   Jon Ison (jison (c) ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

   None
