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

   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. 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

Standard (Mandatory) qualifiers Allowed values Default
[-sequences]
(Parameter 1)
Sequence set filename and optional format, or reference (input USA) Readable set of sequences Required
-descending By default the shortest sequence is given first. Boolean value Yes/No No
[-outseq]
(Parameter 2)
Sequence set(s) filename and optional format (output USA) Writeable sequence(s) <*>.format
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-feature Sequence feature information will be retained if this option is set. Boolean value Yes/No No

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 © 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