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EMBOSS: sizeseq

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:6.4.0.0

   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

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
-sformat1 -sformat_sequences	string	Input sequence format	Any string
-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.

Author(s)

Jon Ison
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

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Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

File: globins.fasta

Output file format

Output files for usage example

File: globins.swiss

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments