                                   twofeat



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Find neighbouring pairs of features in sequence(s)

Description

   twofeat finds neighbouring pairs of specified features in one or more
   input sequences. Each feature may be specified by type, name, sense,
   score, tag/value pairs etc. Their relationship, e.g. their sequence
   separation or overlap, relative sense and order may also be specified.
   It writes a standard EMBOSS report file with any such feature pairs
   identified. By default each pair is written as a single feature but
   (optionally) they are written in their original form.

Algorithm

   For each of the pair of features, you can specify its type name, its
   sense, its score and any tag/value pairs, amongst other things.

   You can then specify the type of relationship that the two features
   should have as follows:

   Minimum and maximum distance between each feature.

   Distance measurement (measure from the nearest ends of the two
   features, from the left ends, from right ends, from the furthest ends.)

   Type of overlap (any type of overlap or no overlap is allowed, Overlap
   required, No overlaps are allowed, Overlap required but one feature
   must not be completely within the other, Feature A must be completely
   enclosed within feature B, Feature B must be completely enclosed within
   feature A).

   Feature sense (any sense, in the same sense or in opposite senses)

   Feature order (any order, Feature A then feature B, Feature B then
   feature A)

   The program proceeds as follows. For eachs sequence: Identify the
   features that match the criteria for Feature A Identify the features
   that match the criteria for Feature B Compare all pairs of features If
   they satisfy the requirements output them to the report file

   By default the resulting pairs of features found are then written to a
   report file as a single feature from the first postion of the left-most
   feature to the last position of the right-most feature. You can modify
   the output to report the pairs of features with no changes made to
   them.

Usage

   Here is a sample session with twofeat

   Without the -twoout option the output report contains just one feature
   for every pair of features found.


% twofeat tembl:x65923
Find neighbouring pairs of features in sequence(s)
Type of first feature [*]: polyA_signal
Type of second feature [*]: polyA_site
The minimum distance between the features [0]: 10
The maximum distance between the features [0]: 50
Output report [x65923.twofeat]:


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

   Example 2

   The -twoout option makes the output report give the pairs of features
   found. The output report format type has been changed to display the
   full original pairs of features in GFF format.


% twofeat -twoout -rformat gff tembl:x65923
Find neighbouring pairs of features in sequence(s)
Type of first feature [*]: polyA_signal
Type of second feature [*]: polyA_site
The minimum distance between the features [0]: 10
The maximum distance between the features [0]: 50
Output report [x65923.twofeat]:


   Go to the output files for this example

Command line arguments

Find neighbouring pairs of features in sequence(s)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -atype              string     [*] By default every feature in the feature
                                  table is allowed. You can set this to be any
                                  feature type you wish to allow.
                                  See http://www.ebi.ac.uk/embl/WebFeat/ for a
                                  list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.org/sprot/userman.html for
                                  a list of the Swissprot feature types.
                                  The type may be wildcarded by using '*'.
                                  If you wish to allow more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron (Any string)
   -btype              string     [*] By default every feature in the feature
                                  table is allowed. You can set this to be any
                                  feature type you wish to allow.
                                  See http://www.ebi.ac.uk/embl/WebFeat/ for a
                                  list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.org/sprot/userman.html for
                                  a list of the Swissprot feature types.
                                  The type may be wildcarded by using '*'.
                                  If you wish to allow more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron (Any string)
   -minrange           integer    [0] If this is greater or equal to
                                  'maxrange', then no min or max range is
                                  specified (Any integer value)
   -maxrange           integer    [0] If this is less than or equal to
                                  'minrange', then no min or max range is
                                  specified (Any integer value)
  [-outfile]           report     [*.twofeat] Output report file name (default
                                  -rformat table)

   Additional (Optional) qualifiers (* if not always prompted):
   -asource            string     [*] By default any feature source in the
                                  feature table is allowed. You can set this
                                  to match any feature source you wish to
                                  allow.
                                  The source name is usually either the name
                                  of the program that detected the feature or
                                  it is the feature table (eg: EMBL) that the
                                  feature came from.
                                  The source may be wildcarded by using '*'.
                                  If you wish to allow more than one source,
                                  separate their names with the character '|',
                                  eg:
                                  gene* | embl (Any string)
   -asense             menu       [0] By default any feature sense is allowed.
                                  You can set this to match the required
                                  sense. (Values: 0 (Any sense); + (Forward
                                  sense); - (Reverse sense))
   -aminscore          float      [0.0] If this is greater than or equal to
                                  the maximum score, then any score is
                                  allowed. (Any numeric value)
   -amaxscore          float      [0.0] If this is less than or equal to the
                                  maximum score, then any score is permitted.
                                  (Any numeric value)
   -atag               string     [*] Tags are the types of extra values that
                                  a feature may have. For example in the EMBL
                                  feature table, a 'CDS' type of feature may
                                  have the tags '/codon', '/codon_start',
                                  '/db_xref', '/EC_number', '/evidence',
                                  '/exception', '/function', '/gene',
                                  '/label', '/map', '/note', '/number',
                                  '/partial', '/product', '/protein_id',
                                  '/pseudo', '/standard_name', '/translation',
                                  '/transl_except', '/transl_table', or
                                  '/usedin'. Some of these tags also have
                                  values, for example '/gene' can have the
                                  value of the gene name.
                                  By default any feature tag in the feature
                                  table is allowed. You can set this to match
                                  any feature tag you wish to allow.
                                  The tag may be wildcarded by using '*'.
                                  If you wish to allow more than one tag,
                                  separate their names with the character '|',
                                  eg:
                                  gene | label (Any string)
   -avalue             string     [*] Tag values are the values associated
                                  with a feature tag. Tags are the types of
                                  extra values that a feature may have. For
                                  example in the EMBL feature table, a 'CDS'
                                  type of feature may have the tags '/codon',
                                  '/codon_start', '/db_xref', '/EC_number',
                                  '/evidence', '/exception', '/function',
                                  '/gene', '/label', '/map', '/note',
                                  '/number', '/partial', '/product',
                                  '/protein_id', '/pseudo', '/standard_name',
                                  '/translation', '/transl_except',
                                  '/transl_table', or '/usedin'. Only some of
                                  these tags can have values, for example
                                  '/gene' can have the value of the gene name.
                                  By default any feature tag value in the
                                  feature table is allowed. You can set this
                                  to match any feature tag value you wish to
                                  allow.
                                  The tag value may be wildcarded by using
                                  '*'.
                                  If you wish to allow more than one tag
                                  value, separate their names with the
                                  character '|', eg:
                                  pax* | 10 (Any string)
   -bsource            string     [*] By default any feature source in the
                                  feature table is allowed. You can set this
                                  to match any feature source you wish to
                                  allow.
                                  The source name is usually either the name
                                  of the program that detected the feature or
                                  it is the feature table (eg: EMBL) that the
                                  feature came from.
                                  The source may be wildcarded by using '*'.
                                  If you wish to allow more than one source,
                                  separate their names with the character '|',
                                  eg:
                                  gene* | embl (Any string)
   -bsense             menu       [0] By default any feature sense is allowed.
                                  You can set this to match the required
                                  sense. (Values: 0 (Any sense); + (Forward
                                  sense); - (Reverse sense))
   -bminscore          float      [0.0] If this is greater than or equal to
                                  the maximum score, then any score is
                                  allowed. (Any numeric value)
   -bmaxscore          float      [0.0] If this is less than or equal to the
                                  maximum score, then any score is permitted.
                                  (Any numeric value)
   -btag               string     [*] Tags are the types of extra values that
                                  a feature may have. For example in the EMBL
                                  feature table, a 'CDS' type of feature may
                                  have the tags '/codon', '/codon_start',
                                  '/db_xref', '/EC_number', '/evidence',
                                  '/exception', '/function', '/gene',
                                  '/label', '/map', '/note', '/number',
                                  '/partial', '/product', '/protein_id',
                                  '/pseudo', '/standard_name', '/translation',
                                  '/transl_except', '/transl_table', or
                                  '/usedin'. Some of these tags also have
                                  values, for example '/gene' can have the
                                  value of the gene name.
                                  By default any feature tag in the feature
                                  table is allowed. You can set this to match
                                  any feature tag you wish to allow.
                                  The tag may be wildcarded by using '*'.
                                  If you wish to allow more than one tag,
                                  separate their names with the character '|',
                                  eg:
                                  gene | label (Any string)
   -bvalue             string     [*] Tag values are the values associated
                                  with a feature tag. Tags are the types of
                                  extra values that a feature may have. For
                                  example in the EMBL feature table, a 'CDS'
                                  type of feature may have the tags '/codon',
                                  '/codon_start', '/db_xref', '/EC_number',
                                  '/evidence', '/exception', '/function',
                                  '/gene', '/label', '/map', '/note',
                                  '/number', '/partial', '/product',
                                  '/protein_id', '/pseudo', '/standard_name',
                                  '/translation', '/transl_except',
                                  '/transl_table', or '/usedin'. Only some of
                                  these tags can have values, for example
                                  '/gene' can have the value of the gene name.
                                  By default any feature tag value in the
                                  feature table is allowed. You can set this
                                  to match any feature tag value you wish to
                                  allow.
                                  The tag value may be wildcarded by using
                                  '*'.
                                  If you wish to allow more than one tag
                                  value, separate their names with the
                                  character '|', eg:
                                  pax* | 10 (Any string)
   -overlap            menu       [A] This allows you to specify the allowed
                                  overlaps of the features A and B.
                                  You can allow any or no overlaps, specify
                                  that they must or must not overlap, that one
                                  must or must not be wholly enclosed within
                                  another feature. (Values: A (Any); O
                                  (Overlap required); NO (No overlaps are
                                  allowed); NW (Overlap required but not
                                  within); AW (A must be all within B); BW (B
                                  must be all within A))
   -rangetype          menu       [N] This allows you to specify the positions
                                  from which the allowed minimum or maximum
                                  distance between the features is measured
                                  (Values: N (From nearest ends); L (From left
                                  ends); R (From right ends); F (From
                                  furthest ends))
   -sense              menu       [A] This allows you to specify the required
                                  sense that the two features must be on. This
                                  is ignored (always 'Any') when looking at
                                  protein sequence features. (Values: A (Any
                                  sense); S (Same sense); O (Opposite sense))
   -order              menu       [A] This allows you to specify the required
                                  order of the two features. The order is
                                  measured from the start positions of the
                                  features. This criterion is always applied
                                  despite the specified overlap type required.
                                  (Values: A (Any); AB (Feature A then
                                  feature B); BA (Feature B then feature A))
   -twoout             toggle     [N] If you set this to be true, then the two
                                  features themselves will be written out. If
                                  it is left as false, then a single feature
                                  will be written out covering the two
                                  features you found.
*  -typeout            string     [misc_feature] If you have specified that
                                  the pairs of features that are found should
                                  be reported as one feature in the ouput,
                                  then you can specify the 'type' name of the
                                  new feature here. By default every feature
                                  in the feature table is allowed. See
                                  http://www.ebi.ac.uk/embl/WebFeat/ for a
                                  list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.org/sprot/userman.html for
                                  a list of the Swissprot feature types. If
                                  you specify an invalid feature type name,
                                  then the default name 'misc_feature' is
                                  used. (Any string)

   Advanced (Unprompted) qualifiers: (none)
   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -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

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   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

   The input is a standard EMBOSS sequence query (also known as a 'USA')
   with associated feature information.

   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: text, html, xml (uniprotxml),
   obo, embl (swissprot)

   Where the sequence format has no feature information, a second file can
   be read to load the feature data. The file is specified with the
   qualifier -ufo xxx and the feature format is specified with the
   qualifier -fformat xxx

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

   See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further
   information on feature formats.

   twofeat reads two sequence inputs with feature information.

  Input files for usage example

   'tembl:x65923' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:x65923

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
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   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the INSDC.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

Output file format

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat 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,
   draw, restrict, excel, feattable, motif, nametable, regions, seqtable,
   simple, srs, table, tagseq.

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   twofeat outputs a report format file. The default format is 'table'.

  Output files for usage example

  File: x65923.twofeat

########################################
# Program: twofeat
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: twofeat
#    [-sequence] tembl:x65923
#    -atype polyA_signal
#    -btype polyA_site
#    -minrange 10
#    -maxrange 50
# Report_format: table
# Report_file: x65923.twofeat
########################################

#=======================================
#
# Sequence: X65923     from: 1   to: 518
# HitCount: 1
#=======================================

  Start     End  Strand   Score starta   enda startb   endb
    484     509       +   0.000    484    489    509    509

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_length: 518
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------

  Output files for usage example 2

  File: x65923.twofeat

##gff-version 3
##sequence-region X65923 1 518
#!Date 2013-07-15
#!Type DNA
#!Source-version EMBOSS 6.6.0.0
X65923  EMBL    polyA_signal_sequence   484     489     .       +       .
ID=X65923.6
X65923  EMBL    polyA_site      509     509     .       +       .       ID=X6592
3.7

Data files

   None.

Notes

   twofeat is intended for use as a simple data-mining tool to enable you
   to look for instances of pairs of features that occur near to each
   other in the same sequence entry.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   There is a slight memory leak that must be fixed at some time. This
   does no affect the results.

See also

                    Program name                   Description
                    extractfeat  Extract features from sequence(s)
                    maskfeat     Write a sequence with masked features
                    showfeat     Display features of a sequence in pretty format

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 (c) emboss.open-bio.org) not to the original author.

History

                    Written (2002) - Gary Williams

Target users

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

Comments

                    None
